Do you switch monitors in between this time? You may want to make a
backup of /etc/X11/xorg.conf (save it in your home directory or
somewhere) and then run

sudo dpkg-reconfigure -phigh xserver-xorg

that will re-configure your xserver settings, which may help you out.

-- 
Resolution not correct in Ubuntu Gutsy
https://bugs.launchpad.net/bugs/188129
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