To reset everything to the defaults, just delete this file:
Vista:
C:\Users\[your windows username here]\AppData\Local\Ironclad Games\Sins of a Solar Empire\Setting\user.setting
XP:
C:\Documents and Settings\[your windows username here]\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Setting\user.setting
Please note that some of these directories are hidden by default. To unhide them, go to Control Panel -> Folder Options -> View and set yourself to view hidden files and folders.