Just to add to this, I am still having the problem with Nautilus on
12.10 i686, and replacing Nautilus by PCManFM as the default file
manager (and tweaking it so it manages the desktop to, as described
here: http://askubuntu.com/a/257456/29270) fixes the problem - PCManFM
always reorganises the icons neatly when changing the screen resolution
without any problem.

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https://bugs.launchpad.net/bugs/1063487

Title:
  Desktop icons/files gets mixed up and overlapped on boot from time to
  time

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