This confused me. I thought that I had left full screen mode because the toolbar appeared, but I actually didn't (there was no "Full Screen" context menu item, the system bar was still missing, and pressing BACK still actually exited full screen mode). I think we just need to be careful to not re-show the browser toolbar on orientation change when we're in full screen mode.
Thinking about this more, should we lock screen orientation in DOM full screen mode? That would fix this issue.