my story:
I use gdm + gnome and upgraded via upgrade manager from 12.10 => 13.04 and also
from 13.04 => 13.10.
It worked for some weeks until a week ago. (GDM screen started but no
loginwindow)
Switching to terminal (CTRL+ALT+F1) worked.
After a long search I found out that switching from gdm to lightdm brought me
back into GUI Mode (sudo dpkg-reconfigure gdm => change to lightdm and reboot)
But then I found out I have permission problems like you described
(Softwarecenter install/uninstall, updates, network, USB)
I tried a lot so I can't be sure what the solution was, but the last things I
tried were:
#19
* (sudo pam-auth-update --force
* reboot
=> did not work
#23
* add
session required pam_loginuid.so
session required pam_systemd.so
to /etc/pam.d/gdm
* dpkg-reconfigure gdm (and select gdm)
* reboot
=> did not work (still no login window)
#23
* add
session required pam_loginuid.so
session required pam_systemd.so
to /etc/pam.d/lightdm
* dpkg-reconfigure gdm (and select lightdm)
* reboot
=> works! I can change network settings, install/uninstall packages, connect
usb devices
#23
* try again "dpkg-reconfigure gdm" (and select gdm)
* (new lines in /etc/pam.d/gdm are already there from previous try)
* reboot
=> works!
I don't know why/how but now also gdm is working again
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