First, Patchwise uses a very straightforward but thorough process of updating files. Files are identified and verified, new updated versions are created and verified, then the old versions are replaced with the new ones.The 1.3 patch *only* changes 6 data files. The engine is untouched, so patching wouldn't affect switching out to the desktop.
So what could be causing your problems? Well, we've always suspected that the NT file system might be causing problems, but we've never had proof. We have no such reservations about FAT32.
Mostly, though, make sure that the OS isn't running a firewall in the background while you're patching -- and maybe while you're playing, as well. We know this has caused problems with WinXP. AV programs might also cause similar problems. I'm presuming that you have plenty of free disk space.
