Comment 5 for bug 2016460

Were you ever able to figure this one out?
I've had the same problem for almost ten years already. The thing is, I use xbindkeys to bind Alt+F4 to close windows. My approach in fixing it is similar to yours: on startup I start xbindkeys, kill it, then start it again. The second time Alt+F4 gets bound correctly.

I am not binding Alt+F4 with Compiz at all. At some point I noticed if I have Chrome open before starting xbindkeys, it has captured Alt+F4 already.

I was never able to figure out a solution even though I've tried every now and then. I'm not sure if this is related to Compiz at all, though.