Sounds like the screen resolution doesn't fit anymore.
Where are the files kept for Sins of a Solar Empire (such as screenshots and such?)
Please note these directories may be Hidden by default. To unhide them, go to your Control Panel -> Folder Options -> View and set yourself to view hidden files and folders.
XP:
C:\Documents and Settings\username\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Setting\user.setting
Vista:
C:\Users\username\AppData\Local\Ironclad Games\Sins of a Solar Empire\Setting\user.setting
Make a backup copy of that file and edit the original with notepad or similar. There are the lines:
VideoFullScreenWidth 1280
VideoFullScreenHeight 800
VideoWindowedWidth 1024
VideoWindowedHeight 768
Change the numbers to fit your screen resolution.
I hope that helps. 
