This issue dates back before upgrading to 8.04, however after upgrading the issue has taken developed further. Before upgrading, my issue was mainly with GDM. It never saved GDM's resolution, or any theme set to it. Now, the same thing happens with the desktop, although it will save a theme if it's one of the default ones apparently.

At any rate, I did check my xorg.conf, only to find unlike other posts, it was missing some sections entirely.

# xorg.conf (xorg X Window System server configuration file)
#
# This file was generated by dexconf, the Debian X Configuration tool, using
# values from the debconf database.
#
# Edit this file with caution, and see the xorg.conf manual page.
# (Type "man xorg.conf" at the shell prompt.)
#
# This file is automatically updated on xserver-xorg package upgrades *only*
# if it has not been modified since the last upgrade of the xserver-xorg
# package.
#
# If you have edited this file but would like it to be automatically updated
# again, run the following command:
# sudo dpkg-reconfigure -phigh xserver-xorg

Section "Files"
EndSection

Section "InputDevice"
Identifier "Generic Keyboard"
Driver "kbd"
Option "CoreKeyboard"
Option "XkbRules" "xorg"
Option "XkbModel" "pc105"
Option "XkbLayout" "es"
EndSection

Section "InputDevice"
Identifier "Configured Mouse"
Driver "mouse"
Option "CorePointer"
Option "Device" "/dev/input/mice"
Option "Protocol" "ImPS/2"
Option "ZAxisMapping" "4 5"
Option "Emulate3Buttons" "true"
EndSection

Section "InputDevice"
Driver "wacom"
Identifier "stylus"
Option "Device" "/dev/input/wacom"
Option "Type" "stylus"
Option "ForceDevice" "ISDV4"# Tablet PC ONLY
EndSection

Section "InputDevice"
Driver "wacom"
Identifier "eraser"
Option "Device" "/dev/input/wacom"
Option "Type" "eraser"
Option "ForceDevice" "ISDV4"# Tablet PC ONLY
EndSection

Section "InputDevice"
Driver "wacom"
Identifier "cursor"
Option "Device" "/dev/input/wacom"
Option "Type" "cursor"
Option "ForceDevice" "ISDV4"# Tablet PC ONLY
EndSection

Section "Device"
Identifier "nVidia Corporation G80 [GeForce 8600 GTS]"
Driver "nvidia"
Busid "PCI:5:0:0"
Option "AddARGBVisuals" "True"
Option "AddARGBGLXVisuals" "True"
Option "NoLogo" "True"
EndSection

Section "Monitor"
Identifier "Generic Monitor"
Option "DPMS"
Horizsync 30-70
Vertrefresh 50-160
EndSection

Section "Screen"
Identifier "Default Screen"
Device "nVidia Corporation G80 [GeForce 8600 GTS]"
Monitor "Generic Monitor"
Defaultdepth 24
EndSection

Section "ServerLayout"
Identifier "Default Layout"
screen "Default Screen"
Inputdevice "Generic Keyboard"
Inputdevice "Configured Mouse"

# Uncomment if you have a wacom tablet
# InputDevice "stylus" "SendCoreEvents"
# InputDevice "cursor" "SendCoreEvents"
# InputDevice "eraser" "SendCoreEvents"
EndSection
Section "Module"
Load "glx"
EndSection
As you can see it has no resolution set or anything. I don't want to mess with it too much, thought I would ask you guys for help first.