i do not believe the macro firing at the same time has any impact.
the issue is that wow is not recognizing that it has lost focus.

please insure you are using v1.8k from 21 june... and not the beta or alpha versions. in the latest stable, i was sending extra killfocus and setfocus messages to the 2 windows

other then that, moving your mouse in and out of those windows, if you have focus-follows-mouse enabled, will usually be enough to push the alt window down to maxfpsbk.