The end result is that the desktop was moved to said folder, I had to change it back and restart explorer.exe to restore it.
It didn't change for the other user on the machine. HijackThis, superantispyware, avg, and malwarebytes came up clean. I tried a sfc /scannow and it found no issues.
This is a Windows 7 x64 install, with UAC enabled. Am I infected? I don't browse the web much on this machine, only used for gaming and occasionally PuTTY, EmacsW32 if I don't want to reboot into OSX. If it's not an infection, I'm not sure what exactly is going on. I really don't even use windows explorer much, save perhaps windows key -> type what I want to open -> enter, so I don't think I dragged anything and 'mv' in cygwin wouldn't mess with the registry, just move the directory, if I had a typo somewhere... Thanks!
Edited by Michael Cohen (mjc), 04 April 2010 - 04:56 PM.