So I solved this issue through another post by lupin about creating a new user in BackTrack. The solution is to perform the following:
cp /etc/skel/.config/menus/applications-kmenuedit.menu ~/.config/menus
This will overwrite your user's menu with the default one from /etc/skel. I performed it, logged out of/into X and everything was back in its correct place.
Thanks lupin!


