Same copy of WoW yes, I was running from two separate directories (and drives) but recently playing on PTR (only one install) I didn't notice a performance cut so I stopped load from different directories. Makes keeping macros, settings and addons working just right even easier.

edit:

And before I was using different directories I still had this issue, but I though it was my own fault as I hadn't upgraded Keyclone (eg Old Bug). Running 1.7u (or whatever it is).