I can confirm the same behaviour (new items appear in "Other") on Fedora
20 with XFCE4:

xfce4-panel-4.10.1-3.fc20.x86_64
alacarte-3.10.0-1.fc20.noarch
gnome-menus-3.10.1-1.fc20.x86_64

The trouble I am having is that the .desktop file is created by alacarte
but the ~/.config/menus/xfce-applications.menu file does not seem to be
updated in the way I would expect. For instance I create a new Item in
the Games menu in alacarte, the generated .desktop file looks like this:

cat ~/.local/share/applications/alacarte-made-1.desktop 
[Desktop Entry]
Comment=fheroes2
Terminal=false
Name=HOMM2
Exec=/home/dan/Games/fheroes2/fheroes2.x86_64
Type=Application
Icon=/home/dan/Games/fheroes2/image/fheroes2_32x32.png

Which is all correct, but I don't see an entry in xfce-applications.menu:
        <Menu>
                <Name>Games</Name>
                <Directory>xfce-games.directory</Directory>
                <Include>
                        <Category>Game</Category>
                </Include>
        </Menu>

If I manually edit the file I can add in the .desktop entry and it will appear 
in the Games menu correctly:
        <Menu>
                <Name>Games</Name>
                <Directory>xfce-games.directory</Directory>
                <Include>
                        <Category>Game</Category>
                        <Filename>alacarte-made-1.desktop</Filename>
                </Include>
        </Menu>

I hope the above explanation is clear as this behaviour is a bit
puzzling to me.

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to the bug report.
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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