I remember seeing this with GNOME on Apple X11 before. Are you starting GNOME from your .xinitrc, or are you starting it manually?
I'm trying to start it with a special .xinitrc.gnome based on the directions in this tip on MacOSXHints:
http://www.macosxhints.com/article.php?story=20040131222238684
specifically I'm using an .xinitrc.gnome which contains this line:
exec /sw/bin/startkde
And using this command to start it.
xinit ~/.xinitrc.kde -- /usr/X11R6/bin/Xnest :3 -geometry 800x600
For testing purposes I often try such things as:
xinit /sw/bin/gnome-session -- /usr/X11R6/bin/Xnest :3 -geometry 800x600+20+50
~Israel~
