is it on all windows including the main or just the alts? If its on the alts, check in Setup -> do-not-pass to see if its in there? Also, check in the key bindings within wow to be sure its not been taken off of move or something like that.
Re the mouse. Is it wireless? I had issues with a wireless mouse on Win7 with Keyclone, and confirmed with Rob that there is a bug with wireless mice in win7.