I have been playing quake3 for more than a year in mandrake 9.0
decided to give gentoo a try installed quake3. But mouse does'nt work.
Works fine on desktop, no idea

Installed mandrake 9.1 the same! Its not the XF86Config-4 because i've tryed several versions
of nvidia drivers and XF86Config is the same as I was running before.

the last straw installed enemy territory and the mouse works perfectly, what could it be the only common denominator I can see are the 2.4.20 kernel 2.4.21 gentoo and mandrake respectively.
where as the mandrake 9.0 kernel is 2.4.19
Beats me!!!!!!!!!!

How can mandrake patch a kernel and call it 2.4.21 when the stable vanilla kernel is 2.4.20 ?
Marketing!

With Quake3, make sure you are running the latest patch which fixes in game mouse issues. I had the same problem in Mandrake 9.1, and this fixed my in game issues. Should be 1.32b which fixes the problems.

thanks works, but why?

It was a flaw in the Point Release patch, so then they released 1.32b to fix it.