This bug has been reported on Ubuntu Launchpad as:
 https://bugs.launchpad.net/bugs/377210

Binary package hint: xfdesktop4

After upgrading from xubuntu Intrepid to Jaunty (xfce 4.6), my right-click desktop menu will no longer show applications at the top level unless I disable file icons on the desktop. Instead, it hides my applications beneath a submenu, effectively putting the single most frequently used menu in my entire windowing system into an rather inconvenient place. Adding insult to injury, the new occupants of the top-level desktop menu are a bunch of commands that I rarely if ever use.

Changing Settings -> Desktop -> Icons -> Icon Type from "file/launcher icons" to "none" restores my applications to the top-level menu, but removes all the file icons from my desktop. Intrepid (xfce 4.4?) let me have both features at once.

This is probably a wishlist item for Xfce 4.6