I've added a debug.err because there seems to be messages about missing files and/or textures which seems odd given that I'm fully updated via SDC, don't use mods (hmm, maybe did a graphics upgrade mod at one point but stopped using it ages ago, maybe even before DA), and haven't altered any files myself. I specifically checked on this one sincce it involves ships:
No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\ShipStyles\*.xml
... look there are lots of xml files in that folder, including the one seemingly for my missing warship (V-CRUISER-02). (I even cut and pastee the path out of winexplorer into the debug.err to make sure my eyes weren't deceiving me on the path

).
All of my other ships are fine - and they're all custom designs (constructor, miner, troop transport).
I'm tempted to re-install. :-/
Debug Message: Version v1.61 Dark Avatar last updated on: Wed Jun 13 14:10:36 2007
Debug Message: Checking DX Version.
Debug Message: *********DXDiag info follows.*********
System Info
Time: 9/3/2007, 20:03:46
DirectX Version: DirectX 9.0c (4.09.0000.0904)
Machine Name: PWNETTLE2
Operating System: Windows XP Professional (5.1, Build 2600) Service Pack 2 (2600.xpsp_sp2_gdr.070227-2254)
Languages: English (Regional Setting: English)
System Manufacturer: Gigabyte Technology Co., Ltd.
System Model: P35-DS3R
BIOS: Award Modular BIOS v6.00PG
Processor: Intel(R) Core(TM)2 Duo CPU E6750 @ 2.66GHz (2 CPUs)
Physical Memory: 3070MB RAM
Page File: 203MB used, 4753MB available
Windows Dir: C:\WINDOWS
Display Info
Display device 1:
Device Name: \\.\DISPLAY1
Card Name: NVIDIA GeForce 8800 GTS
Manufacturer: NVIDIA
Chip Type: GeForce 8800 GTS
DAC Type: Integrated RAMDAC
Key Device: Enum\PCI\VEN_10DE&DEV_0193&SUBSYS_042110DE&REV_A2
Display Memory: 640.0 MB
Current Display Mode: 1920 x 1200 (32 bit) (60Hz)
Monitor Name: SyncMaster 244T(Digital)
Monitor Max Resolution: 1920,1200
Driver Name: nv4_disp.dll
Driver Version: 6.14.0011.6218
Driver Date: 6/29/2007 00:43:00
DirectX Acceleration Enabled: Yes
Sound info
Sound device 1:
Description: Sound Blaster Audigy
Default Sound Playback: Yes
Default Voice Playback: Yes
Hardware ID: PCI\VEN_1102&DEV_0007&SUBSYS_100A1102&REV_00
Manufacturer ID: 1
Product ID: 100
Driver Name: P17.sys
Provider: CREATIVE
Driver Version: 5.12.0001.0608
Driver Date: 3/17/2006 16:10:00
Type: WDM
Other Drivers:
Acceleration Level: 3
Cap Flags: 0
Min/Max Sample Rate: 0, 0
Sound device 1:
Description: Line 6 PODxt Live
Default Sound Playback: No
Default Voice Playback: No
Hardware ID: USB\Vid_0e41&Pid_4650&Rev_0001
Manufacturer ID: 1
Product ID: 100
Driver Name: L6PODLV.sys
Provider: Line 6
Driver Version: 2.06.0008.0000
Driver Date: 5/4/2005 16:46:30
Type: WDM
Other Drivers:
Acceleration Level: 3
Cap Flags: 0
Min/Max Sample Rate: 0, 0
Debug Message: *********END dxdiag info.*********
Debug Message: Entering WinMain
Debug Message: ******* Starting Game Shell *******
Debug Message: Going Fullscreen
Debug Message: Preparing to change display settings.
Debug Message: Using hardware vertex processing
Debug Message: Using multilsample setting: D3DMULTISAMPLE_4_SAMPLES
Debug Message: Game Resolution: 1920 x 1200
Debug Message: Running fullscreen.
Debug Message: HAL (hw vp): NVIDIA GeForce 8800 GTS
Debug Message: D3DPRESENT_INTERVAL_DEFAULT
Debug Message: Refresh rate: 60
Debug Message: Bit Depth: 32 bit.
Debug Message: *********Checking D3DDevice Caps***********************
Debug Message: A full-color cursor is supported in hardware at high resolution modes.
Debug Message: RGB in format 6:6:6, Masks reported as ff0000:ff00:ff
Debug Message: Now Fullscreen
Debug Message: Shell initialization complete
Debug Message: GalCiv2 is activated.
Debug Message: ***** Initializing Game *****
Debug Message: Timer Frequency is 0 369e99
Debug Message: Initializing sound card.
Debug Message: initailizing bink
Debug Message: No files found matching mask Movies\techs\*.bik
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Gfx\Movies\*.bik
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\sfx\*.wav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Music\*.mp3
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Event Music\*.mp3
Debug Message: Create setup screens.
Debug Message: Clear galaxy settings.
Debug Message: Clear influence.
Debug Message: Clear up laws.
Debug Message: Clear first time events.
Debug Message: Clear wonders and trade goods.
Debug Message: Clear sector mapper.
Debug Message: Set mouse.
Debug Message: Set update timer.
Debug Message: Popup Manager Update: Updating window with ID=0
Debug Message: Popup Manager Update: Unhiding FullscreenBink
Debug Message: Clear data definitions.
Debug Message: Killing ship styles:
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\ShipStyles\*.xml
Debug Message: No files found matching mask ./Data/\FleetFormations\*.fleet
Debug Message: No files found matching mask Gfx\Planets\C0*.png
Debug Message: No files found matching mask gfx/Terrain/1SideN*.png
Debug Message: No files found matching mask gfx/Terrain/1SideE*.png
Debug Message: No files found matching mask gfx/Terrain/1SideS*.png
Debug Message: No files found matching mask gfx/Terrain/1SideW*.png
Debug Message: No files found matching mask gfx/Terrain/2SideN*.png
Debug Message: No files found matching mask gfx/Terrain/2SideE*.png
Debug Message: No files found matching mask gfx/Terrain/2SideS*.png
Debug Message: No files found matching mask gfx/Terrain/2SideW*.png
Debug Message: No files found matching mask gfx/Terrain/3SideN*.png
Debug Message: No files found matching mask gfx/Terrain/3SideE*.png
Debug Message: No files found matching mask gfx/Terrain/3SideS*.png
Debug Message: No files found matching mask gfx/Terrain/3SideW*.png
Debug Message: No files found matching mask gfx/Terrain/4SideN*.png
Debug Message: No files found matching mask gfx/Terrain/4SideE*.png
Debug Message: No files found matching mask gfx/Terrain/4SideS*.png
Debug Message: No files found matching mask gfx/Terrain/4SideW*.png
Debug Message: Reading Star Names
Debug Message: Reading Star Names... Done
Debug Message: No files found matching mask ./Data/English/Tutorials/*.xml
Debug Message: Popup Manager Update: Updating window with ID=1
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Dark Avatar\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Dread Lords Campaign\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Gfx\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Metaverse\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\SandboxGames\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\ships\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\ShipStyles\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\shiptemplates\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Story Logs\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\temp\*.sav
Debug Message: Killing threads.
Debug Message: Kiling civs.
Debug Message: Killing ships.
Debug Message: Killing rallypoints.
Debug Message: Killing misc objects.
Debug Message: Killing stars.
Debug Message: Killing anomalies.
Debug Message: Killing asteroid fields.
Debug Message: Killing asteroid field mining bases.
Debug Message: Killing space resources.
Debug Message: Killing colonies and planets.
Debug Message: killing scenario.
Debug Message: Clearing Turn Event Log
Debug Message: Clear galaxy settings.
Debug Message: Clear influence.
Debug Message: Clear up laws.
Debug Message: Clear first time events.
Debug Message: Clear wonders and trade goods.
Debug Message: Clear sector mapper.
Debug Message: Loading Custom Map
Debug Message: Loading Data Defs
Debug Message: Clear data definitions.
Debug Message: Killing ship styles:
Debug Message: Loading TechDefs
Debug Message: Max num techs: 273
Debug Message: Loading ImprovementDB
Debug Message: Loading Component Defs
Debug Message: Loading ShipTypes
Debug Message: Loading ShipTemplates
Debug Message: Loading ParsedHardpoints
Debug Message: Loading AnomalyTypes
Debug Message: Loading RandomEvents
Debug Message: Loading UPIssues
Debug Message: Loading ResourceTypes
Debug Message: Loading InvasionTactics
Debug Message: Loading SBmodules
Debug Message: Loading PoliticalParties
Debug Message: Loading Planet Types
Debug Message: Loading Star Types
Debug Message: Loading AFMBModules
Debug Message: Loading ShipStyles
Debug Message: Loading Game
Debug Message: Loading: Game mode is normal.
Debug Message: Loading Galaxy
Debug Message: Sectors across: 5 x 5
Debug Message: Loading FOW Map
Debug Message: Loading ZOC Map
Debug Message: Loading Planets
Debug Message: Loading Stars
Debug Message: Loading Anomalies
Debug Message: Loading Resources
Debug Message: Loading AsteroidFields
Debug Message: Loading AFMiningBases
Debug Message: Loading Civs
Debug Message: Loading Colonies
Debug Message: Loading RallyPoints
Debug Message: Loading Ships
Debug Message: Loading Fleets
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Loading Turn Event Log
Debug Message: Loading Treaties
Debug Message: Loading ENDGALAXYDATA
Debug Message: Updating ZOC.
Debug Message: UIBeginGame called with g_ulLocalPlayerID = 5
Debug Message: UIBeginGameHelper: New Game Started
Debug Message: UIBeginGameHelper: Mods are Disabled
Debug Message: Popup Manager Update: Updating window with ID=20
Debug Message: Popup Manager Update: Unhiding QuarterlyWnd
Debug Message: Popup Manager Update: Updating window with ID=16
Debug Message: Game Screen: Setting mode to 2
Debug Message: Popup Manager Update: Unhiding ResearchWnd
Debug Message: Game Screen: Setting mode to 9
Debug Message: Game Screen: Setting mode to 0
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Popup Manager Update: Updating window with ID=45
*DEBUG ERROR: ***FleetManagerWnd: Unknown edit field FleetMan_Stacked_List_Entry type: CustomListBoxEntry ***
*DEBUG ERROR: ***FleetManagerWnd: Unknown edit field FleetMan_Fleet_List_Entry type: CustomListBoxEntry ***
Debug Message: FleetManagerWnd: Cannot find OBJID FleetMan_All_Shield_Image
Debug Message: Popup Manager Update: Unhiding FleetManagerWnd
Debug Message: Destroying ship Voqarians Fleet 132. Orbiting: 0
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Cannot find texture
Debug Message: Error flipping back buffer to primary buffer.
Debug Message: D3DERR_DEVICELOST
Debug Message: Device lost
Debug Message: Attempting to reset device.
Debug Message: Error flipping back buffer to primary buffer.
Debug Message: D3DERR_DEVICELOST
Debug Message: Device lost
Debug Message: Attempting to reset device.
Debug Message: Popup Manager Update: Updating window with ID=28
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Dark Avatar\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Dread Lords Campaign\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Gfx\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Metaverse\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\SandboxGames\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\ships\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\ShipStyles\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\shiptemplates\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\Story Logs\*.sav
Debug Message: No files found matching mask C:\Documents and Settings\Paul\My Documents\My Games\GC2DarkAvatar\temp\*.sav
Debug Message: Popup Manager Update: Unhiding SaveGameWnd
Debug Message: Killing threads.
Debug Message: Kiling civs.
Debug Message: Killing ships.
Debug Message: Killing rallypoints.
Debug Message: Killing misc objects.
Debug Message: Killing stars.
Debug Message: Killing anomalies.
Debug Message: Killing asteroid fields.
Debug Message: Killing asteroid field mining bases.
Debug Message: Killing space resources.
Debug Message: Killing colonies and planets.
Debug Message: killing scenario.
Debug Message: Clearing Turn Event Log
Debug Message: Clear galaxy settings.
Debug Message: Clear influence.
Debug Message: Clear up laws.
Debug Message: Clear first time events.
Debug Message: Clear wonders and trade goods.
Debug Message: Clear sector mapper.
Debug Message: Loading Custom Map
Debug Message: Loading Data Defs
Debug Message: Clear data definitions.
Debug Message: Killing ship styles:
Debug Message: Loading TechDefs
Debug Message: Max num techs: 273
Debug Message: Loading ImprovementDB
Debug Message: Loading Component Defs
Debug Message: Loading ShipTypes
Debug Message: Loading ShipTemplates
Debug Message: Loading ParsedHardpoints
Debug Message: Loading AnomalyTypes
Debug Message: Loading RandomEvents
Debug Message: Loading UPIssues
Debug Message: Loading ResourceTypes
Debug Message: Loading InvasionTactics
Debug Message: Loading SBmodules
Debug Message: Loading PoliticalParties
Debug Message: Loading Planet Types
Debug Message: Loading Star Types
Debug Message: Loading AFMBModules
Debug Message: Loading ShipStyles
Debug Message: Loading Game
Debug Message: Loading: Game mode is normal.
Debug Message: Loading Galaxy
Debug Message: Sectors across: 5 x 5
Debug Message: Loading FOW Map
Debug Message: Loading ZOC Map
Debug Message: Loading Planets
Debug Message: Loading Stars
Debug Message: Loading Anomalies
Debug Message: Loading Resources
Debug Message: Loading AsteroidFields
Debug Message: Loading AFMiningBases
Debug Message: Loading Civs
Debug Message: Loading Colonies
Debug Message: Loading RallyPoints
Debug Message: Loading Ships
Debug Message: Loading Fleets
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Can't find ship type Fleet in definitions
Debug Message: Loading Turn Event Log
Debug Message: Loading Treaties
Debug Message: Loading ENDGALAXYDATA
Debug Message: Updating ZOC.
Debug Message: UIBeginGame called with g_ulLocalPlayerID = 5
Debug Message: UIBeginGameHelper: New Game Started
Debug Message: UIBeginGameHelper: Mods are Disabled
Debug Message: Popup Manager Update: Updating window with ID=20
Debug Message: Popup Manager Update: Unhiding QuarterlyWnd
Debug Message: Popup Manager Update: Updating window with ID=16
Debug Message: Game Screen: Setting mode to 2
Debug Message: Popup Manager Update: Unhiding ResearchWnd
Debug Message: Game Screen: Setting mode to 9
Debug Message: Game Screen: Setting mode to 0
Debug Message: WM_CLOSE message received.
Debug Message: GameUninitialize start
Debug Message: Killing Galaxy
Debug Message: Killing threads.
Debug Message: Kiling civs.
Debug Message: Killing ships.
Debug Message: Killing rallypoints.
Debug Message: Killing misc objects.
Debug Message: Killing stars.
Debug Message: Killing anomalies.
Debug Message: Killing asteroid fields.
Debug Message: Killing asteroid field mining bases.
Debug Message: Killing space resources.
Debug Message: Killing colonies and planets.
Debug Message: killing scenario.
Debug Message: Clearing Turn Event Log
Debug Message: Clear galaxy settings.
Debug Message: Clear influence.
Debug Message: Clear up laws.
Debug Message: Clear first time events.
Debug Message: Clear wonders and trade goods.
Debug Message: Clear sector mapper.
Debug Message: Clear data definitions.
Debug Message: Killing ship styles:
Debug Message: Killing Galaxy: Completed
Debug Message: Shutting down sound system.
Debug Message: Clearing sound and music handles.
Debug Message: PlanetTex_C:\Program Files\Stardock\TotalGaming\GalCiv2\Data\HeightMaps\p10_h2_w512_h256_2027473779.raw_HeavyGravityWorld not cleared 1 counts left.
Debug Message: WorkAreaBack.png not cleared 1 counts left.
Debug Message: GameUninitialize end
Debug Message: Device not cleared. 14713 counts left.
Debug Message: D3D not cleared. 1 counts left.
Debug Message: Destroying Window.
Debug Message: Main Shell terminating normally