I got the bug again, this time I saved, alt-tabbed to check the debug.err, alt tab back in, saved and quit the game.
I'll post some snippets of the log here:
Debug Message: Version v1.80f Twilight of the Arnor beta 3b last updated on: Thu Dec 6 11:50:39 2007
Debug Message: Checking DX Version.
Debug Message: *********DXDiag info follows.*********
System Info
Time: 12/20/2007, 19:18:53
DirectX Version: DirectX 9.0c (4.09.0000.0904)
Machine Name: MARK
Operating System: Windows XP Professional (5.1, Build 2600) Service Pack 2 (2600.xpsp_sp2_gdr.070227-2254)
Languages: Dutch (Regional Setting: Dutch)
System Manufacturer: MICRO-STAR INTERNATIONAL CO.,LTD
System Model: MS-7360
BIOS: Default System BIOS
Processor: Intel(R) Core(TM)2 Duo CPU E6750 @ 2.66GHz (2 CPUs)
Physical Memory: 2048MB RAM
Page File: 382MB used, 3560MB available
Windows Dir: C:\WINDOWS
Display Info
Display device 1:
Device Name: \\.\DISPLAY1
Card Name: Radeon X1950 Series
Manufacturer: ATI Technologies Inc.
Chip Type: ATI Radeon Graphics Processor (0x7244)
DAC Type: Internal DAC(400MHz)
Key Device: Enum\PCI\VEN_1002&DEV_7244&SUBSYS_0B121002&REV_00
Display Memory: 256.0 MB
Current Display Mode: 1280 x 1024 (32 bit) (75Hz)
Monitor Name: Plug en Play-monitor
Monitor Max Resolution: 1600,1200
Driver Name: ati2dvag.dll
Driver Version: 6.14.0010.6727
Driver Date: 9/29/2007 04:06:17
DirectX Acceleration Enabled: Yes
Sound info
Sound device 1:
Description: SB X-Fi Audio [EC00]
Default Sound Playback: Yes
Default Voice Playback: Yes
Hardware ID: PCI\VEN_1102&DEV_0005&SUBSYS_00211102&REV_00
Manufacturer ID: 1
Product ID: 100
Driver Name: ctaud2k.sys
Provider: Creative
Driver Version: 5.12.0001.1187
Driver Date: 8/17/2006 10:17:10
Type: WDM
Other Drivers:
Acceleration Level: 3
Cap Flags: 0
Min/Max Sample Rate: 0, 0
--- some non related (?) stuff ---
Debug Message: Destroying ship Constructor MK6 13338. Orbiting: 0
Debug Message: Destroying ship Constructor MK6 13345. Orbiting: 0
Debug Message: Destroying ship Constructor MK6 13346. Orbiting: 0
Debug Message: Destroying ship Constructor MK5 13327. Orbiting: 0
Debug Message: Destroying ship Constructor MK6 13352. Orbiting: 0
Debug Message: ***Attacker Korath Clan has courage bonus 0
Defender Iconian Refuge has courage bonus 10.
//It always happens when someone attacks a ship orbiting a planet)
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
--- some more of latter ---
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Destroying ship Iconian Defender M9 v34 13355. Orbiting: 1
Debug Message: Was Orbiting: Epsilon V
//I'm guessing this is from the planet above,
//just a bunch of lines of debug between them

Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
--- some more of latter ---
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Save Game: About to save
Debug Message: Saving game D:\\My Games\GC2TwilightArnor\QuickSave.tmp
Debug Message: Num Sectors Across: 8
Debug Message: Saving: Game mode is normal.
Debug Message: Number of ships: 207, Number of Fleets: 18
Debug Message: Save game finished.
// saving the game 1st time
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
--- some more of latter ---
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Error flipping back buffer to primary buffer.
Debug Message: D3DERR_DEVICELOST
Debug Message: Device lost
Debug Message: Attempting to reset device.
//I alt-tabbed back into the game
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
--- some more of latter ---
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Save Game: About to save
Debug Message: Saving game D:\\My Games\GC2TwilightArnor\QuickSave.tmp
Debug Message: Num Sectors Across: 8
Debug Message: Saving: Game mode is normal.
Debug Message: Number of ships: 207, Number of Fleets: 18
Debug Message: Save game finished.
// save the game 2nd time
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
--- some more of latter ---
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: OptionsWnd: Quit Btn
// guessing cos i quit the game
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Out of sample handles.
--- some more of latter ---
ebug Message: Out of sample handles.
Debug Message: Out of sample handles.
Debug Message: Posting WM_CLOSE message.
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: Desplay_Scroll_Small_Tab.png not cleared 2 counts left.
Debug Message: Desplay_ShipList_Entry_Down.png not cleared 98 counts left.
Debug Message: Desplay_ShipList_Entry_Over.png not cleared 98 counts left.
Debug Message: Desplay_ShipList_Entry_Up.png not cleared 196 counts left.
Debug Message: Desplay_Small_Status_Frame_Up.png not cleared 196 counts left.
Debug Message: Gfx\Planets\Iconia.png not cleared 1 counts left.
Debug Message: Gfx\Planets\Kryseth.PNG not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetBarren_1.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetHighGravity_4.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetOceanic_4.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualGood_1.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualGood_2.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualGood_3.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualGood_5.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualGreat_1.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualMed_1.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualMed_2.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualMed_3.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualPoor_1.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualPoor_2.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualPoor_3.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetQualPoor_4.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetRadioactive_1.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetRadioactive_2.png not cleared 1 counts left.
Debug Message: Gfx\Planets\PlanetToxic_3.png not cleared 1 counts left.
Debug Message: Gfx\Planets\Toria.png not cleared 1 counts left.
Debug Message: TextFiledBack.png not cleared 197 counts left.
Debug Message: WorkAreaBack.png not cleared 1 counts left.
Debug Message: GameUninitialize end
Debug Message: Device not cleared. 148530 counts left.
Debug Message: D3D not cleared. 1 counts left.
Debug Message: Destroying Window.
Debug Message: Main Shell terminating normally
Debug Message: Unallocated Mem: 8 bytes of memory from line 1130 of .\Source\editfields.cpp
Debug Message: Unallocated Mem: 8 bytes of memory from line 1130 of .\Source\editfields.cpp
--- some more of latter ---