I was having a lot of trouble with NetworkManager not saving my VPN group and user passwords. I'm guessing this is a bug and I did see some references to launchpad bugs while doing my googling to find a solution. However, it took me a while to figure it out. It requires a little editing of the system-connection files.
If you look in
/etc/NetworkManager/system-connections/, you will see your connection files. Open one of them and change a few of the settings. The two settings I had to change/add were: