uhm, well....
I only get mouse problems when running Nexuiz. No other app/game behaves that way. And Im pretty sure my (good old) mouse is still ok - Im using it every day without any trouble, except in Nex'. Another mouse, hmm, I have a kind of adapter to plug the one I have in as an usb-device... dont think that will help, but Im trying.
I remeber I had a similar issue with other OpenGL- and SDL-based games. The effect You describe to exit and restart the app/game did work back then, but I didnt encounter that behaviour for quiete a while now, only in Nexuiz.
specs...
Im playing Nexuiz compiled from cvs/svn, which I update&compile every few weeks...
My system basically is a Debian (mostly) testing, with kernel 2.6.17 and libc6 2.3.6-15 (all debian packages).
sdl-libs versions:
sdl-image: 1.2.5-2
sdl-mixer: 1.2.6-1.1+b1
sdl-net: 1.2.5-7
sdl-sound: 1.0.1-9+b1
libsdl1.2-dev: 1.2.10-3
sdl-gfx1.2: 2.0.13-2
Xorg: 7.0.22 - Ill skip the 100 packages for each X-component here...
and of course the nvidia-driver: 1.0.8762-2, same as kernel module, the kernel module was compiled i686, gcc 4.0.4 20060507 (prerelease) (Debian 4.0.3-3), same as version as used to compile the kernel.
I really dont think this is a hardware-issue, as I would have strange effects in other apps as well, so Ill omit my hardware-specs here, but If You really want to hear about that, Ill post them too.