I was having the same problem described here, exactly.  The krandrtray
workaround worked; running xrandr -s 1680x1050 (in my case) worked; but
I didn't like the way the login started out wrong, and then flickered a
bit after logging in before the resolution was right.

However, I managed to solve the problem.  In my case I didn't have my
native resolution listed in xorg.conf; the first problem was that I
didn't have the right modeline defined.  I did some searching and found
a discussion where it was pointed out that since X was getting the right
settings eventually, the correct modeline ended up in my X logs
(/var/logs/Xorg.0.log in my case).  There were multiple log lines that
looked like the following:

(II) intel(0): Modeline "1680x1050"x0.0  119.23  1680 1728 1760 1840
1050 1052 1058 1080 -hsync -vsync

...which is very close to the format needed for xorg.conf.  Here's what
I ended up with in xorg.conf, showing only the relevant lines; I only
added the ModeLine line and the "1680x1050" mode (the rest was already
there from a configuration utility I used):

Section "Monitor"
  Identifier "Monitor0"
    Option "DPMS" "true"
  HorizSync    28.0 - 96.0 # Warning: This may fry old Monitors
  VertRefresh  50.0 - 75.0 # Very conservative. May flicker.
  ModeLine "1680x1050"  119.23  1680 1728 1760 1840  1050 1052 1058 1080  
-HSync -Vsync # added this
EndSection

Section "Screen"
  Identifier "Screen0"
  Device     "Card0"
  Monitor    "Monitor0"
  DefaultColorDepth 16
  SubSection "Display"
    Depth     1
    Modes "1680x1050" "1024x768" "800x600" "640x480" # added "1680x1050" - the 
rest were here
  EndSubSection
  # more subsections like the above, but repeated for color depths of 4, 8, 15, 
16, 24, and 32
EndSection

(I fully realize that no one else will need these exact settings--but
hopefully the general idea proves useful to someone.)

Anyway, once I (a) had the correct modeline in xorg.conf, and (b) added
the new mode to the "Screen" section, my resolution was correct from the
login screen, with no workarounds necessary and no resetting of the
resolution.  The problem was gone.

I'm running Arch (just installed); I don't know how other distributions
handle xorg.conf stuff.  (I tried looking at an xorg.conf from Ubuntu,
but it was practically empy...they must do it somewhere else.)  But
regardless of how you do it, I think that if you can get your xorg setup
to recognize the resolution from the get-go, it won't keep switching
back to something else until you open the Display panel in System
Settings.

-- 
Screen Resolution is not being restored after relogin
https://bugs.launchpad.net/bugs/268434
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