I upgraded to Ubuntu 12.04 recently and for some reason it broke Gnome 3. The shell doesn't start up at login. My .xsession-errors looks like this right after I log in:

gnome-session[1689]: WARNING: Session 'gnome' runnable check failed: Timed out

(gnome-settings-daemon:1744): color-plugin-WARNING **: failed to get edid: 
unable to get EDID for output

(gnome-settings-daemon:1744): color-plugin-WARNING **: unable to get EDID 
for xrandr-default: unable to get EDID for output

(gnome-settings-daemon:1744): color-plugin-WARNING **: failed to reset 
xrandr-default gamma tables: gamma size is zero
** Message: applet now removed from the notification area
** Message: using fallback from indicator to GtkStatusIcon
** Message: moving back from GtkStatusIcon to indicator

Then I can run gnome-shell --replace, the shell starts up and everything works. This is what I get immediately after:

Window manager warning: Log level 16: Unable to register authentication agent: 
GDBus.Error:org.freedesktop.PolicyKit1.Error.Failed: An authentication agent already 
exists for the given subject
Window manager warning: Log level 16: Error registering polkit authentication agent: 
GDBus.Error:org.freedesktop.PolicyKit1.Error.Failed: An authentication agent already 
exists for the given subject (polkit-error-quark 0)

(gnome-shell:2442): folks-WARNING **: Failed to find primary PersonaStore with type 
ID 'eds' and ID 'system'.
Individuals will not be linked properly and creating new links between Personas will 
not work.
The configured primary PersonaStore's backend may not be installed. If you are 
unsure, check with your distribution 

Also, if I run /usr/lib/nux/unity_support_test -p, everything comes back as Yes and this checks out:

OpenGL vendor string:   NVIDIA Corporation
OpenGL renderer string: GeForce 8300 GS/PCIe/SSE2
OpenGL version string:  3.3.0 NVIDIA 295.40

It isn't a huge problem since I can get gnome shell to work, but it is a little annoying. So, I'd like to fix this. Thanks for your help.