if you have installed wow each time then each client will patch normally however if like me (and presumably Beyond-tec) you just copied the directories then there will only be one entry in the registry and the patch will only path the instance that is in that location.

any chance someone with multiple installations can export their blizzard key? sanitised of course. just so I can see how multiple instances work?

atm I just have 3 reg files on my desktop and merge each one in turn, applying the patch