games now freeze! hardware prob? PLZ HELP

The games that run on my little sister's computer have started lagging, this is what happens.

The game will run, and run fine.. then all of a sudden the sound will start skipping and cracking and then the game itself will lag for a few moments and then start running perfect again. Then it starts happening more often and the lag becomes worse when it happens. I scanned her computer for viruses and found that it had TONS of them.. after getting rid of most of the viruses the problem remained, so i reformated her entire computer and the problem still occurs, here is some info that is important

-Computer is two years old
-Compaq Presario 5000
-Pentium 3 1.4ghz proc
-NVIDIA GeForce 2 (fully updated drivers)
-Latest version of direct X
-The games meet her system requirements
-Only happens with games
-The games used to run FINE in the past
-It happens with all games new and old

I've tried everything i could think of, but its still happening. One of my friends told me it may be a hardware problem, like the motherboard might be going? I called compaq and of course they refused to help me because the computer is no longer under warranty.

I personally have no idea, the weird thing is the games used to run fine and now they are having that problem, so i figured it may have been a vid card or sound card problem, but i got the latest drivers reinstalled both of them, and it still occurs. If anyone has ANY ideas whatsoever just list them, i'll try anything, ive been working on this damn thing for days and its driving me nuts, if any of you have younger siblings u know how annoying they can be when they need something fixed.

Make sure the Direct X and other video drivers are up-to-date first of all.

When you did a format, did you wipe the drive clean (using FDISK) and reformat/reinstall that way, or did you just use a system restore disk? I'd recommend reformatting making sure to kill the partition first.

If hardware is going, most likely you're not going to see performance issues in a game. Either it works or it doesn't.

I used a factory disk to reformat my computer back to its original settings, which leaves me with a question. When i did that her computer should act the way it did when we first got it... which would mean the games work.. but that isnt the case.