I have just upgraded to alacarte-3.11.91-1.fc21 (installed locally by
downloading the RPM from the Rawhide repository) and the issue is now
fixed. It seems the solution is just to update alacarte to the latest
version. From the alacarte 3.11.91 changelog:

Changes:
        Drop Help button
        Ensure items have valid Exec
        Add a man page
        Make Restore button work again
        Fix createing menus
        Fix creating items

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https://bugs.launchpad.net/bugs/1245315

Title:
  alacarte fails to write a proper "Categories=<>;" line to .desktop
  files

Status in “alacarte” package in Ubuntu:
  Confirmed

Bug description:
  When creating a new menu entry in the Applications Menu of Xubuntu
  using the Alacarte Menu Editor (alacarte 3.10.0-1) then alacarte does
  not enable the writing of a "Categories=<>;" attribute in the new
  .desktop file created in /home/<>/local/share/applications/.

  Without a recognized and meaningful "Categories=<>;" attribute, the
  new menu entry is relegated by default to the non-specific "Other"
  menu category in the Applications Menu of Xubuntu.

  Moving the newly-created menu entry in question to a more meaningful
  Applications Menu category (such as, eg, "Applications", "Office",
  "Systems", etc) by dragging and dropping then fails in alacarte due to
  the very absence of any "Categories=<>;" attribute in the .desktop
  file.

  Instead,

  First, when creating a new menu entry in, for example, "Applications",
  then alacarte should write a corresponding "Categories=<>;" attribute
  line in the newly-made .desktop file.

  Second, when dragging and dropping the newly-created menu entry in
  alacarte from, for example, "Applications" to, for instance, "System",
  then alacarte should amend the "Categories=<>;" attribute line in the
  .desktop file accordingly.

  
  Note 1: If alacarte cannot do these things automatically, then it should at 
least allow the user to choose the Application Menu category, say, from a 
drop-down list, when creating or editing a menu entry, and write this choice to 
the corresponding .desktop file in the form of a suitable "Categories=<>;" 
attribute line.

  Note 2: Resolving this issue by manually editing .desktop files, of
  course, wholly defeats the very raison d'être of Menu Editor programs
  such as alacarte.

  
  --
  System: xubuntu 13.10 32-bit fully up-to-date

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