Here are the steps to reproduce the problem :

Steps 0-8 just create a new menu item.

   1. Start with a newly installed Ubuntu 10.04 (64 bit). Gnome.
   2. Select menu System ->Preferences->Main Menu.
   3. Select “Applications” on the left.
   4. Click on “New Menu” button.
   5. Enter “gksudo nautilus” in both fields. Click”OK”.
   6. Select the “gksudo nautilus” menu.
   7. Click “New Item”.
   8. Again (just for simplicity) in all fields enter “gksudo nautilus”. A new item is created. You could also see that the new menu and the item are available in the Applications menu and work fine.
      The goal is to make this new menu entry available for all users. As expected the steps above create three files under my home directory:
         1. ~/.local/share/applications/alacarte-made.desktop
         2. ~/.local/share/desktop-directories/alacarte-made.directory
         3. ~/.config/menus/applications.menu
            They now should be moved to a common location which is accessible for all the users.
   9. In accordance with the spec (http://standards.freedesktop.org/menu-spec/1.0/), move the alacarte-made.desktop file to directory /usr/share/applications.
  10. Everything still looks and works fine, just as expected. But here is the problem.
  11. If you now reboot your 64 bit system the menu item would not show up any longer. The only way I found to see the menu entry again is to open the /usr/share/applications/alacarte-made.desktop file and to add a space and save it ( this works only till the next reboot). I tried to 'touch' the file but it did not help.
  12. The above steps work fine on my 32 bit Ubuntu 10.04 or in KDE. In both of these cases the menu item stays there after the system is rebooted.