In my Whiskermenu pre-installed applications are not shown. After a reinstall of for example Gimp Whisker could not find it either. The xfce4-popup-applicationswindow too did not show them.
I tried resetting by pkill xconfd and deleting xfce4 in ~/.config/ and a restart.
I use UbuntuStudio 16.04 which is like Xubuntu but with a custom theme and some software for music and art creation.
Delete the file /home/username/.config/menus/xfce-applications.menu. This file is created when you use the menu-editor. After deleting the file all applications will show up in the menu, but Favorites will be empty, you can easily repopulate by adding favorites. Don't use the menu-editor, it always leads to loss of menu-entries.
If you can't open Thunar from the menu, open terminal with Ctrl+Alt+T and use command rm ~/.config/menus/xfce-applications.menu
