I think (but I'm not sure) missing windows borders may also occur without compiz. Occasionally it occurs on starting X, and I don't think I have ever had to restart X more than once (CTRL-ALT-BACKSP) to get it up correctly.
If you have compiz running, it's easy to go into the settings manager and disable animation, wobbling etc. I always do, but I may use the cube thing. Wish I had a simpler alternative to compiz for doing that.