I'm experiencing the same issue with a fresh installation of intrepid.
Connections not marked system are retained, but those marked system are
not. Additionally, a 'non-system' setting can not be changed to system -
this setting is also lost.
$ dpkg -l network-manager* | grep ^ii
ii network-manager 0.7~~svn20081018t105859-0ubuntu1
network management framework daemon
ii network-manager-gnome 0.7~~svn20081020t000444-0ubuntu1
network management framework (GNOME frontend
ii network-manager-openvpn 0.7~~svn20081015t024626-0ubuntu1
network management framework (OpenVPN plugin
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network-manager issues with system settings AND secrets (Was: doesn't save wep
key on a "system setting" connection)
https://bugs.launchpad.net/bugs/281711
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