hi there myfokkinnick@yahoo.i,
which pointrelease of Quake 3 (Arena I suppose) did you use or did you even use a pointrelease at all?
Supposely lots of people have experienced mouse issues with Quake 3 Arena and that's why there are several
linuxq3apoint-1.32b.x86.run point releases. I've had mouse issues as well until I grabbed me all the 1.32b pointreleases.
The latest one is
linuxq3apoint-1.32b-3.x86.run which you also can get from here:
http://www.slackmagic.com/gaming/
It should fix many if not most of the issues you may have especially dealing with your mouse.
Good luck & happy fragging!