I am using the 2012 x64 subscription Advantage, service pack 1 ( I hope that is the lastest).
I think this is happening when I have multi views. I noticed that even the command "FrameSelected" does not update the active window.
I also tested using "getPanel -wf" to see if some other window had focus, but it seems like there must be part of the gui that is grabbing events.
I will have to try Justin's idea with the timeline.
:)