The hildon-desktop in the CSSU has the option of disabling desktop editing. This includes getting to the theme menu and views list etc. from the desktop.

Basically, disables exactly what you're reporting as not working.

Run:
This will list the majority of the custom hildon-desktop's gconf settings (all the ones in that gconf folder - note that gconf's folders are not in the same location in the "real" file system). There's a wiki page and another page on Matan's site that lists all the options at what they do, but for now you just want the one that's called "disable_edit". So you could just run:
If it reports "false", the problem is elsewhere. If it's true, then the problem is what I thought - at some point this dbus key was set (maybe you had Matan's desktop mods some time long ago or whatever), or something set it for some wierd reason at some point. Anyway, to set it back to false, to enable desktop edits, use:
Don't run it as root, run it as user. Running as root shouldn't cause any problems, but it might save some file as root and that might mess things up later. (Very unlikely though, afaik.)