Various programs hang, can't really get more descriptive

We're doing what we can over here, but we're running out of options. Many windows programs, and 3rd party programs like Skype, Steam, etc (But not all) are hanging when launched, or shortly after launching. That or they crash instantly. Nothing is logged to the Event Viewer, and Memtest comes out clean. We can't run chkdsk because it's one of the ones that just hangs, we've run Malwarebytes, Spybot S&D, and AVG Free but the best they could do was some adware and a few cookies.

Our next idea is to run the startup recovery from the windows 7 disk, and then after that try to run chkdsk from the windows disk's command prompt.

Known programs that hang:
Skype
Steam
Most games
Shutdown
Chkdsk
System Recovery
Windows Update

Those last two really limit our options here.

We've also noticed that his cmd prompt doesn't run anything at all, so there might be something up with his environment variables, but we couldn't find anything out of the ordinary (%SYSTEMROOT%/Windows/System32 and wbem are there as normal, and the files themselves are fine)

Boot into safemode and then run chkdsk.

The computer has simply decided to start working fine again. We ran chkdsk from the windows installation disk, and it came up nice and clean, and the System Repair on the disk also detected no problems. The only actual differences were the cleaned up stuff from Spybot, which required a restart to clear and was running a new scan while I was writing this post, and we unplugged a wired xbox controller that had a headset plugged in, which he was using as his main audio source.

It was either some of the adware that was in memory and required a restart to clean, or a driver conflict through the controller. Both of which really make no sense, why would adware or a sound driver break things like System Restore and Windows Update? I'm not entirely convinced the problem is fixed.