I've noticed the ubuntu panels can disappear and not reappear after I switch between single window and unity modes. They don't reappear with full screen mode either. If I "show taskbar in unity" the panels persist. across modes.
You're sure Tools are up to date and running (e.g. if you took a kernel update, you reconfigured Tools)? By panels, do you mean the top and bottom system bars?
Sounds like karmic koala, that's the kernel level on my copy of 9.10. I get my menu bar and bottom panel back switching from Unity and back. I added a top panel below the menu bar and it redraws exiting Unity.
