Have a look in the ~/.config/menus/ for previous copies of applications.menu and compare then to see what's changed. if you have anything, you could try renaming one of them as applications.menu and see if that makes things better.

I have had a quick look and found this link:

The suggested 'worst case' solution is to delete ~/.config/menus/applications.menu and ~/.config/menus/setting.menu
to reset the entire menu.

This should then re-create the standard menus and then you can configure to taste with the main menu app.

Hope it works