this is a generic long-time windows problem, not specific to altbinz or any one software,
when that happens, what you can do is the following:
while the 'focus' is on the application window you are trying to get back hit:
alt-space..
arrow down..
enter..
now hit a couple of the arrow buttons to nudge the window around a little bit..
then use your mouse to move the app's window back to a reasonable position in the screen.
and hit enter again when you're done.