One thing that might help you is that all hotkey and other settings are stored in a Game.prefs file.
If I remember right can be found ~users/steamuser/Local Settings/Application Data/Gas Powered Games/Supreme Commander Forged Alliance/Game.prefs (but I play on Linux so on windows it might be a slightly different location).
Either way you can open it with notepad and mess around with settings that sounds like they might fix your problem (after making a little backup of the file ofcourse).
Alternatively you can delete it and I'm pretty sure that on startup of FA it will be regenerated with all settings to default, WHICH MEANS YOU LOSE YOUR HOTKEY SETTINGS but possibly also the problem you are having with your mouse.
I have no idea if it will fix your issue, but it's probably worth a try.