I just tested this out with Games for Linux 7.0.0 on Ubuntu 8.04; When I run TF2 in fullscreen mode the gnome bars on the top and bottom of the screen are shown overtop of the game, additionally the mouse doesn't line up with the items in the game screens.
I am running an Inspiron 9300 laptop with nVidia GO 6800 video card (256MB) and a 1.8 GHz Intel Processor.
Anyone else have this problem? I didn't see anything in open/closed bug reports and was thinking about submitting it.