polkitd(authority=local): Operator of unix-session:c34 FAILED to authenticate to gain authorization for action org.freedesktop.policykit.exec for unix-process
sudo still works. So it's most probably a gnome issue, and as it wokrd before using gdm3setup it most probably a gdm3setup issue.
Reinstalling gnome helped once, using gdm3setup breaks it again.
If more infos are needed i'll provide them gladly.
I have tested under ArchLinux and Ubututu Gnome 13.10 without problem with pkexec. It's probably a bug with polkit/policykit. Try if another application that use polkit cause a problem.
The message in the auth.log is like
sudo still works. So it's most probably a gnome issue, and as it wokrd before using gdm3setup it most probably a gdm3setup issue.
Reinstalling gnome helped once, using gdm3setup breaks it again.
If more infos are needed i'll provide them gladly.