You are right about the mouse settings
I've noticed this too.
I've found that only restarting the game fixes this stuff.
With some unlagged stuff the standard sens of 5 changes to about 3.. like rudyrailer posted. One thing I havent figured out is that my cl_yawspeed and sometimes cl_pitchspeed changes to some crazy value (default is 140 i think).
Maybe the mouse feeling is different due to non custom resolution in minimized mode.
Try in_mouse 1 (or -1) then in_restart.
The gamma issue is something you will probably be able to figure out. When you change to minimized mode your desktop maybe bright if your gamma is more than 1. To work with normal gamma then either set it at 1 and vid_restart or do r_ignorehwgamma 1.
Sometimes you can have conflicting settings where the game thinks its in full screen mode when its in window mode.. this screws up gamma when you revert back to full screen and the gamma in game goes low and when you quit the game the desktop gamma is so bright it could burn holes in your monitor
You can reset this in display properties (select 3d/opengl properties?) and you can reset it there instead of rebooting).
A clean way to fix this would be to have your own config file which you can exec. That way your good config is guaranteed to load correctly. If you launch the game then your default q3config.cfg might remember some bad settings (such as it loading in window but thinks its full screen). I think this can happen if it crashes.
