Hey, if you're re-releasing, mind making sure /home/user/.xbindkeysrc.scm is not owned by root this time?
We might be able make application windows avoid it, either by setting it up as a panel (with some WM hints, I guess...) or by making a panel under it of an appropriate size? Just a thought I had yesterday, and I can't be the first, so there's probably a good reason it's not been implemented yet...