Bryce -- it appears that this is intimately related to the other bug I reported 
where X stopped working entirely -- That is bug # 152678.  I have attached 
several xorg.conf files and Xorg.0.log files there.  I've been thrashing on 
this and can give you the scenario a little more explicitly.
(repeat  of my info there)
I've determined that my particular problem is caused by this sequence:
1 -- editing xorg.conf to add the line Virtual 1600 1200 (or replacing with one 
that is correct)
2 -- booting or restarting X -- gdm gives login, login results in a screen not 
using the virtual size, rather the physical size.
3 -- running the 'Screens and Graphics' tool and selecting the 1600x1200 
screen. This comes up and works correctly. However -- the xorg.conf file is 
destroyed at this point.
Subsequent boots or x restart are mixed. I've had them totally lock, come up in 
640x480 mode, and really be a mess or fail to work entirely. With no xorg.conf 
it does come up in a crippled (no 1600x1200 virtual window) but useable mode. 
As long as I don't try to use the xorg.conf file that Screens and Graphics 
poops out I can replace it with a good file and then run. I have determined 
that if i use xdm instead of gdm it respects my xorg.conf virtual setting. In 
this scenario, the only downside is needing to use 'shutdown -h now' to stop my 
session.

This bug is actually two interrelated bugs.

1: gdm does not respect the xorg.conf 'virtual' line.
2: displayconfig-gtk has no clue as to dealing with the 'virtual' line and 
totally screws up what it writes

At this point deleting the xorg.conf file results in a limited display
that can be used for troubleshooting (although not my real work). I am
assuming that this is your interest. If so, my congratulations on
getting something that works this well.

I've completely deleted gdm from my machine.

I've managed to free up another 3 g partiton and will install the
release ISO there and report if I still have problems.  In addition will
peruse the wiki information.

If there are particular files generated under particular conditions,
I'll be delighted to send them to you.

-- 
'Virtual' screensize lost on upgrade
https://bugs.launchpad.net/bugs/152757
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