How are you changing focus?

Isboxer wizard by default sets a macro to run on window swaps which changes the active window to jamba master, so is it possible that this is changing your master separately to however you are changing focus?

Can't offer too much more than that at the moment because I have been running FTL now for a while. When I ran a focus setup, my focus change macro was set into my window swap hotkeys so that window swaps occurred in conjunction with master and focus swaps anyway.