Just lost a day to this myself (though my fault for not keeping
backups).

A permissions (or configuration, I suppose) error anywhere in the gconf
hierarchy can turn this up.

In my case, /etc/gconf/2/path included references to the following
(installed automatically at some point):

xml:readonly:/etc/gconf/gconf.xml.system
xml:readonly:/var/lib/gconf/debian.defaults
xml:readonly:/var/lib/gconf/defaults

As it turned out, /var/lib/gconf/debian.defaults was not world-readable.


The only clue logged regarding this was:

===
The files that contain your preference settings are currently in use.

You might be logged in to a session from another computer, and the other
login session is using your preference settings files.

You can continue to use the current session, but this might cause
temporary problems with the preference settings in the other session.

Do you want to continue? Continue (y/n)
===

in /var/log/gdm/:0-greeter.log.  Not exactly the first place I would
look, or the clearest indication of where the problem is.  (After
numerous attempts to reinstall and reconfigure all related packages, I
was hunting for lockfiles...)


IIRC it looks like fresh installs (or 100% fresh installs of gconf) may not 
include /etc/gconf/2/path at all (or delete it?), so the wrong permissions from 
whatever package installs /var/lib/gconf/debian.defaults may only turn up for 
upgrading users.

-- 
GDM fails to authenticate pre-existent users.
https://bugs.launchpad.net/bugs/432492
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Desktop Bugs, which is a bug assignee.

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