CS:S massive fps decrease

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So my computer with AMD phenom 9600 quad-core processor 2.30GHz, 8G ram, 64 bit vista OS, and Nvidia GeForce 8800 GT. Used to run at about 60+ FPS while moving. However I got a worm, named VBS.runauto. And as all the ways said online wouldn't work and norton and windows defender both failed to get rid of it i used the factory reset disks that came with my computer.

After updating all my drivers and directX and such my computer now runs CS:S at about 40-20 if staying still and drops to below 5 fps when moving as well as telling me I only have 4 gigs of ram. I am absolutely confused, tried reinstalling CS and the drivers and it has made no difference whatsoever. And was hoping someone around me could help... Happy holidays btw.
 
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