Windows 7 seems to be running sluggish after updates??

I installed windows7 on my brother in laws computer. It seems that after doing updates it runs sluggish and the windows are slow as hell to respond when you click on them, If I click a box in a open window the bar at the top of the window goes transparent and it loses all functionality.If I move the pointer back to the top of the window and right click like a mofo it lights back up and I regain functionality and can finaly click what ever box I was originaly trying to click in the first place. Im sure it's not a hardware issue as the comp is a xfx 780I sli mobo,2.66 core 2 duo,WD500 gig hd with 32 mb of cache,8 gigs of ocz ddr3 platnum ram,2 9800 gt's in sli and a enermax 595w ps.
I at first thought it could be a heat issue or bios setting I might have missed. The cpu has been repasted using arctic cool paste, the bios settings have been checked 12-15 times. so Im confident it isnt a hardware issue. for programs it has windows7 pro oem,nero9 reloaded,avast anti virus,u torrent and dvd shrink installed. I have uninstalled every update except the critical and security ones. Has anyone else had this issue? Is there a known problem with a update that I dont seem to know about yet?
Is this just a quirk of W7 that I didnt notice during the beta test?
Oh and I have gone to the hardware manufacturers web sites and downloaded and installed the latest driver and bios updates for the hard ware.
I have put about 30 hours into this computer and am still no farther ahead than when this started. can anyone help?