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After installing F9, I am running X at 1440x900. My /etc/X11/xorg.conf has exactly one entry for 24 bit color depth - "1440x900". However, when I restart the system or logout, the GDM session resets to 800x600 mode and the display goes a bit odd (refresh rate I suspect).
Since GDM and X are supposedly sharing the xorg.conf file, how could gdm be getting an 800x600 setting since there isn't one in my xorg.conf?
BTW - if I reinstall my F7 disk, both are displaying at 1440x900.
I don't use the same distro as you (I've got Debian) but your issue has something in common with one of mine, so I'll dexcribe it in case it might help point you in the right direction.
After upgrading by changing from the 'i810' graphics driver to the 'intel' driver, which works with the xrandr ('X Rotate AND Resize) utility, the following has happened:
When using an external LCD display with my laptop I initially achieved the max resolution of the external display (i.e. 1680x1050). However, suddenly now Gnome starts every time with a lower resolution 1250xsomething.
When I issue the command:
it reports 1680x1050 as the next available resolution above the active one. I can switch to it without any trouble by issuing:
$xrandr -s 1680x1050
However, I have not found out what the source of the problem is. Changing xorg.conf to specify only the wanted resolution does not solve the problem. Pretty annoying!
I am guessing there must be some other file in addition to xorg.conf that stores information that is used when starting the GUI.
Maybe you could check documentation on the exact order of processes and config files that are invoked when starting the GUI with your distribution?