If this is indeed the gconf keys, it's all a matter of what the applet tries to do with them when converting them to system-level connections.
Steve, after stopping nm-applet, can you try to modify the "/apps/nm-applet/stamp" value to "2" then restarting it on the command-line? This should retry the conversion from gconf to keyfiles, and maybe seeing what's happening on the command-line will give clues as to what the problem is.
If this is indeed the gconf keys, it's all a matter of what the applet tries to do with them when converting them to system-level connections.
Steve, after stopping nm-applet, can you try to modify the "/apps/ nm-applet/ stamp" value to "2" then restarting it on the command-line? This should retry the conversion from gconf to keyfiles, and maybe seeing what's happening on the command-line will give clues as to what the problem is.