Files with "QuickTime" in the name disappearing

This is the first time I've ever seen this. I'm a customer support technician at a university and a student brought in a laptop where "iTunes wasn't working". It was packed with virii and spyware, which we removed. The computer now checks out completely using every scan we can come up with. That said, iTunes still doesn't work (it opens up with no errors, but pressing play doesn't cause the song to start playing--play button doesn't switch to pause, etc.). So, following the troubleshooting page at apple.com/support I went to check out the QuickTime control panel...but it wasn't there. So, I went to check the QuickTime folder at C:\Program Files\QuickTime...and it wasn't there. So, I checked the Add & Remove Programs control panel and QuickTime showed up. I uninstalled it and iTunes. Reinstalled. Same deal. It gets weirder.
I tried downloading the standalone QuickTime installer, but when I plugged in my USB flash drive to copy the installer over...it didn't show up. Eject it, plug it back into my computer...and it shows up. So, I created a text file on the laptop in question and named it "QuickTimeInstaller.txt" and it instantly disappeared once the rename took effect. The first thing that comes to mind is a virus, but I have scoured the web and can't find any mention of a virus that specifically targets QuickTime like this.
Has anyone run into a problem like this before?
-Joel

I'm not too sure how a standalone install will help being as this problem persists after doing a complete uninstall of both QuickTime and iTunes. When trying to copy the standalone installer over, it disappears. I can rename it and it shows up just fine, but I fail to see how simply doing a reinstall with a standalone installer will resolve the problem. At this point we're very close to simply rebuilding the computer.

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