Comment 5 for bug 326120

Interesting and frightening, Jeff. I wasn't aware of window stacking being dependent on the video driver.

I should have been more specific before: commit http://bazaar.launchpad.net/~onboard/onboard/trunk/revision/897 tries to keep Onboard on top of full-screen windows only in compiz/unity and only with "force to top" mode enabled.
I'm not aware of a solution for unity-2d, unfortunately. However, seeing that unity-2d is gone from Quantal, we may not have to find one anymore.

You can try trunk, but on Precise you'll probably run into problems due to the shift to Python3. We were planning to release a version compatible with Precise eventually, though..