I have used Unity for a bit, but I have never encountered this.
Any full screen (games, lock screen, etc) app, the Unity sidebar and the top bar are always visible. Thankfully, they don't work. However, working on a Netbook using a full-screen app and losing 5% of your screen is rather annoying.
(For some reason I can't post screenshots atm)
Is there any way this can be fixed? I am running 12.04