Comment 1 for bug 443433

Workaround:
 1) Run gconf-editor (Alt+F2, and type "gconf-editor")
 2) Navigate to /apps/netbook-launcher/favorites. Make sure "favorites" is highlighted.
 3) In the right pane, there should be a key called "favorites_list". Right-click it and choose "Edit key"
 4) This brings up a list of apps -- reorder them as desired. (Selecting a listing and click the "Up" or "Down" buttons.) [ SEE NOTE BELOW]
 5) Once you've gotten the list to your liking, run "killall netbook-launcher" in Alt+F2. (This forces the Netbook Remix to restart and re-read its configuration)
 6) Click the Ubuntu menu-button in the upper-left corner -- that should now bring up Netbook Remix, now with your updated Favorites ordering.

NOTE: In step 4, if you've added custom (non-default) apps to Favorites, they'll be named e.g. "app 0", "app 1", etc. You can see which apps these are by selecting their corresponding entries in the left pane of gconf-editor, inside of "favorites", and looking at what shows up in the right pane. (For me, the "app 0" folder has a key that says "desktop_file" / " /usr/share/applications/gnome-terminal.desktop". So that means it's the Terminal app.)