I tested it with a Ubuntu 11.10 Live CD x64 and a fresh install on my HDD:
After starting Tomboy I cannot logout / shutdown / restart anymore. The menu bar / launcher disappears after initiating the logout but the Desktop background won't disappear. Windows remain open but do loose their window decorations...
Tested with Unity 2D / 3D.
Running Ubuntu on a Toshiba P835 with Intel HD 3000, so it would be great if somebody could confirm this, before I can post this to launchpad.
Edit: Since it was confirmed I opened a bug on launchpad: bug #883370. Please vote to get this fixed soon!
There are bugs already related to my problem at bugzilla