32-bit apps fail silently on 64-bit Windows 7

Very strange problem. I recently cleaned a client's HP Windows 7 Home system from a malware infection and the computer is in a rather odd state. It will run any 64-bit application, but will not run any 32-bit app. It took me about an hour to notice that there were no processes in Task Manager tagged *32. There also aren't a hell of a lot of native 64-bit apps on Windows 7 either. If I run task manager while trying to run a 32-bit app, the app shows up in task manager for a fraction of a second and then disappears. No errors displayed, nothing in the event viewer. The five (or six) WOW64 executables and DLLs in System32 all have the correct size and date, although I have not yet tried replacing them with the files from a known good system. The next step is to try a repair installation from the recovery partition. I've done a fairly bit of Googling and have found nothing close to what we are seeing. Any suggestions or pointers would be appreciated. At this point, I'm expecting to have to reinstall Windows 7, but I would love to figure how what is actually wrong with the system in case it ever happens again. Thoughts?

Mahalo!

Sorry, I should have mentioned that I already ran sfc /scannow, although not in safe mode. It found no errors or problems.

The system has three updates queued up, but all fail because the updates themselves are or contain 32-bit programs. I thought at first that the system might have a rootkit infection. Unfortunately TDSSKiller.exe is also a 32-bit application. I concur that the 32-bit emulator has gotten stomped on somehow. The trick is to figure out how to unstomp it. Replace the *WOW64*.* in System32? Fairly easy. Replace all 5GB+ of \Windows\SysWOW64\? Somewhat less pleasant.

Do a system restore: System Restore