Just to discard some obvious thing, how are you going into X? Are you using some display manager (xdm, kdm, gdm, slim, entrance, etc.)? Or are you using an .xinitrc file?
In the former case, can you try a different login manager?
In the later case, can you post the contents of your ~/.xinitrc?
On a related note, and since this seems to be related to user permissions in some way, can you check these few things:
- USE="consolekit policykit udev dbus" emerge -auDvN world, does it report anything?
- rc-update show | grep consolekit, is it listed there?
- if not, do "rc-update add consolekit default" and "/etc/init.d/consolekit start", then restart X or your display manager.