I have seen the same problem (I do not know if it is related to GDM, but
this is with hardy).

At the moment it's particularly bad; .Xauthority reverts to root:root
within a second of changing it by hand to user:user.

It seems to be atieventsd which is the trigger of this (but possibly not
the cause; I tried strace on it but it didn't seem to call chown
itself). When I stop it, .Xauthority stays as user:user.

-- 
After gdm upgrade no X cliens can be run
https://bugs.launchpad.net/bugs/196464
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