Maybe you have a wrong resolution in a Modes line of the file
/etc/X11/XF86Config-4.
For example, with the Mode line below, I think I would get the effect
you describe. Leaving out the resolution "1280x960", which is wrong for
my monitor, would fix it.
SubSection "Display"
Depth 24
Modes "1280x960" "1280x1024" "800x600" "640x480"
EndSubSection
I think I use /etc/X11/xorg.conf file.
the Modes line shows: "1024x768" "1600x1200" "800x600" "640x480"
Correct if you ask me...
On the other hand, could it be that GDM still uses the XF86Config-4
file and gnome the xorg.conf file? Probably a silly thaught. But the
XF86Config-4 file is still resident.