strange problem with performance

Ok, I have recently reformatted my computer. the only programs i have installed are avg, firefox and 2 AAA games. i have the updated video card drivers as well. My set up is a Intel core i7 2.8ghz, i have 4 gigs of ram, and a geforce 8800gts, my mobo is a msi p55-gd65. i have been experience slow down in games that never occurred before the reformat. Because of this i checked my windows experience index it has my base score at 2.9. the readout is as follows

Processor 3.8
Memory 5.1
Graphics 2.9
Gaming Graphics 6.4
Primary hard disk 5.6

Im feeling like something is wrong with windows relative to the processor and graphics this is so strange to me because i wasnt having this problem before i reformatted and i'm 99% sure that my experience index scores were much higher.

yes, i have done all of those things my computer is free from viruses and there are no yellow marks over anything in device manager.

by clean boot you mean simply restarting my computer? or reformatting? because iv done both. as of now im running CPU-Z and prime 95. my CPU usage is maxed out at 100% however my core speed is holding at 524 and my multiplier is at 4x. even when running some of my AAA titles in windows mode my speed wont break 1600 and my multiplier wont break 14x. BIOS maybe?

in wouldnt trust the windows experiance thingy , download and run 3d mark 06 (free version) , set everything to low in your driver control panel first , then post up all your scores from 3 runs , cpu score shader model 2 and 3 score etc.

then we can determine exactly whats causing the issue , cpu or gpu and get some software running ingame (MSI Afterburner) to see exactly whats going on withn your hardware when under load , it may be your gpu downclocking it may be your cpu spiking but the we need to know where to start , so 3d mark scores please 3 runs

one more thing , are you sure all you have done is reformatted , have you added/installed anything (no matter how insignificant you masy think it is) at all or have you been into your bios?