Comment 14 for bug 1000500

I have ubuntu 12.04.
I had this problem and found I had changed my startup applications menu a few days before. To fix click on the start button in top right corner then select to startup applications and restart your computer after changing..
make sure the follow boxes are checked:
Certificate and key storage
Gnome settings daemon
policykit authentication agent
SSH key agent
This allowed me to install my updates, open package manager and install software from software center.
When I unchecked these 4 boxes I lost the root rights. After checking the boxes and retarting they all worked fine.
Hope this helps.
RR