I am also having this problem and it is relentless. I have had to halt my conquering of the Arceans as I can not get my ships to their worlds! I'm using version 1.80g.100 Dark Avatar. I thought I'd post here instead of creating a new post to save clutter.
Fleet movement bug only exists in 1.80e; it's fixed in 1.80g. SDC is lying to you. Change your HKEY_LOCAL_MACHINE\SOFTWARE\Stardock\Drengin.net\GalCiv2\DarkAvatar Version string to something other than 1.8.x (1.7 will work just fine), and then update. Or, this file will do it for you. I'm unsure if this is an SDC-specific problem (the version string alone would seem to present itself as global), but it may be worth giving Impulse a shot to update it if you have not already done so.
If you are for some reason seeing this bug in a version that shows 1.80g in the title bar in your taskbar, I would suggest doing a full reinstall of DA (DL should not be necessary).
