I'm on: Linux localhost.localdomain 4.2.7-300.fc23.x86_64 #1 SMP Wed Dec 9 22:28:30 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux and am running the gnome shell:
gdm       5357  0.0  0.3 1664896 12440 tty1    Sl+  Dec19   1:44  |           \_ gnome-shell --mode=gdm --wayland --display-server
patrick  18408  4.7  7.7 2118460 301800 tty2   Sl+  Dec19 709:00              \_ gnome-shell --sm-client-id 10c611b43929bd837e144347998690676200000033080000


When the Applications Menu extension is turned on, the Applications menu doesn't show any content for: Sound & Video, Graphics, Internet, Programming, System Tools, Universal Access menu items. The lines on the Applications menu are there, but when hovering over them they don't get the grey highlight box and the sub menu of desktop items with the appropriate category do not show up.

The Application menu works fine for: Favorites, Accessories, Education, Games, Office, Sundry, Utilities, Wine, and Other. Those items highlight when hovering over them, and a sub menu with desktop items with the appropriate category show up.

These XDG environment variables are set in my environment:
DG_VTNR=2
XDG_SESSION_ID=1
XDG_MENU_PREFIX=gnome-
XDG_SESSION_TYPE=x11
XDG_SEAT=seat0
XDG_SESSION_DESKTOP=gnome
XDG_RUNTIME_DIR=/run/user/1000
XDG_CURRENT_DESKTOP=GNOME

~/.local/share/applications and ~/.local/share/desktop-directories have been moved away.

I've looked through the entries in /etc/xdg/menus, /usr/share/applications, and /usr/share/desktop-directories and everything seems to be up to the appropriate freedesktop.org specs.

A different extension, Frippery applications menu, is able to display everything as expected, but boy is it annoying.

The Applications Menu extension used to work on my machine, but sometime in the last few months it quit.

I am pretty tech savvy so anything you might want to ask to get more information and debug this is great with me. I've been a system programmer since the late 80s.