from a terminal, see if it helps---it should put compiz managing your windows again, if it isn't for some reason (obviously you need to have Compiz installed and working). If it doesn't help, you can try falling back to Metacity by using
metacity --replace &
Or if you use Emerald, you could run it's similar replace command to make it take control of your window borders. I haven't lost the borders often, but those times I have, this has worked.
Hope it helps