The up2date desktop file never got updated to include the right categories. Should be Categories=X-Red-Hat-Base;Application;SystemSetup; Also, you really don't need to use desktop-file-install (doesn't need munging) since the desktop file in CVS is correct, but that's neither here nor there :)
should be fixed in 3.0.15 or higher
Change confirmed with 3.1.15-7. Although it appears we are still using desktop-file-install with this code, but not sure if that's really pressing or not.