Try going to Documents>AppData>Local>Ironclad Games>Sins of a Solar empire>Setting
And open User.SETTING file with notepad or something and edit some of the settings you see there
I haven't tried this yet but it may fix up your settings.
Also.... Maybe deleting it will Set your game to default settings, but make sure you back it up
Since i have never tried this. and is also too lazy to trouble shoot it (sorry lol)
-You have to have "show hidden files" on under folder options in control panel