I use ROX instead of GNOME; compiz seems to have some problems with its panels. The panels have GDK_WINDOW_TYPE_HINT_DOCK set on them and they also have struts set for them to avoid being covered by other windows. The main problem is that panels on the left or top (so I guess the problem must have something to do with the offset being from 0) have their own strut applied to them so there's a gap between them and the edge of the screen. I'll attach a screenshot of my panel near (supposed to be *at*) the top. Panels on the right and bottom edges are handled correctly in this respect. It happens both in Debian unstable on my desktop (amd64, NVidia proprietary driver) and Ubuntu Gutsy on my laptop (IA32, open ATI driver).

I also have problems with one or more of my panels disappearing altogether occasionally, and one of them was flickering for a while.

AFAIK ROX uses a screen-sized window for its backdrop whereas I think nautilus uses the root window. Could this have anything to do with either problem?