Additional information: Booting with a different set of monitors (one display instead of two) definitely triggers it: After login the system freezes and the checksum of the user file differs afterwards. It's impossible to start the desktop session with a (usually working) file for a setup with two displays. The only workaround is to have two different config files that have to be swapped depending on the environment (2 or 1 display after bootup) prior to gui login.
An additional error and probably user file corruption is a font problem that can occur while changing dconf settings. Some menu fonts are rendered abnormal (or the wrong type? They're thinner than before) at once without reason. This can't be reversed, any further configuration and rebooting has no effect. Only deleting the user file and doing all the set up again helps - with luck the file doesn't corrupt this time. Note: Since this happens using MATE could it also be related to the mate-settings-daemon resp. mate-settings-daemon-gstreamer which is using the dconf-gsettings-backend? It has caused trouble in the past but I don't know how dconf and the daemon interact (well I assume whatever a daemon does with the dconf-gsettings-backend it should never produce a corrupted config file, so this would still be a dconf bug).
