I dont know what happened to me but it seems that something around the AGP/Graphics system broke.
When I put everything together and reinstalled Windows I was getting around 40+ FPS in Doom3, every game ran smoothly and fast. Now I was benchmarking again, doing some test between Linux (Gentoo AMD64) and Windows and I see that I am getting 27 FPS in Doom 3 using exactly the same settings. I think well lets try putting everything in default(removing overclock and all), to my surpirse I still get 27 FPS. I try some settings in the BIOS, enabling FastWrites, changing AGP mod, changing aperture size, nothing makes a difference, 27 FPS. This is very strange stuff, no matter at what speed I run my CPU I get 27 FPS in Doom 3 under Linux or Windows. I conclude that there is some problem around the Graphics subsystem.
Can anyone please help me? Lydia?