See instructions here for replacing hildon-desktop:

http://talk.maemo.org/showthread.php?t=38314

(no need for following the dbus-scripts instructions, if you are not intereseted in keyboard operation).

The order in hildon.menu is still ignored. The way to set the order is to add a X-Osso-User-Position= line in .desktop and .directory files. Smaller numbers appear first.