It's basically how AHK 'sees' the clients, it depends on which client it grabs first and enters into the wowid Array. So you have to have checks in place which the lastest version of my Duel Account Controller has. It is the best way i've found so far.

Basically what happens is you start multi WOW's

%wowid1% = Main Window
%wowid2% = Clone

but next time it is like this

%wowid1% = Clone
%wowid2% = Main Window


Which is why my script minimizes both copies, then maximizes one and asks the user if this is the MAIN if not, then it assumes the other is.

Trust me I wish there was a Sure-Fire better way to do things