IMHO the problem is probably having different graphics settings on the windows. Each window needs to have the same settings, otherwise the card will have trouble. I don't see how it could do things like AA/AF on just part of the screen without alot of slowdown. I would recommend having the draw distance maxed, but all other settings as low as possible.

Having each wow on a seperate hard drive will only help load times. Your framerate should not be affected ... unless you run out of RAM and it has to start paging.