I run four separate WoW installations on one of my computers. I patched one copy (copied the patch files from my fifth installation on my main computer to the slave computer)and had to copy the patched copy to completely new directories for it to work for me (i.e., copying over my unpatched directories failed). Dunno why it didn't work just copying over my current installations, but I got it working so I never bothered to think much about it.