I've got an alternative explanation for what's going wrong here. The
default GNOME session runs gnome-session and this in turn runs
/etc/gdm/Xsession as mentioned in comment #14. As pointed out there,
/etc/gdm/Xsession runs through the session scripts in
/etc/X11/Xsession.d. This includes 50x11-common_determine-startup which
should cause ~/.xsession to be picked up. What's going wrong is that a
set of environment variables that are normally set by /etc/X11/Xsession
are not set by /etc/gdm/Xsession, including things like USERXSESSION. So
when the scripts run they don't behave as designed.

A simple kludge to get things working is to observe that
/etc/gdm/Xsession sources /etc/xprofile and ~/.xprofile very early on,
and we can use one of these files to set the environment up correctly
for the Xsession.d scripts. Stick the attached script into /etc/xprofile
(or ~/.xprofile) and see if that gets .xsession working again. It works
for my dot files that depend on .xsessionrc getting sourced.

I'm not sure what a more correct fix would look like as I haven't delved
into which files are sourced from Debian/Ubuntu sources and which are
from upstream (and hence less favourable for changes).

** Attachment added: "xprofile script fragment to set up environment for 
Xsession.d scripts"
   http://launchpadlibrarian.net/36633221/xprofile

-- 
The new gdm doesn't give an option to use .xsession
https://bugs.launchpad.net/bugs/398300
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