I think I might have hit a bug in mintMenu - Elysa main edition.
1. You need two accounts for this, one has sudo access (probably the first account you created after install) - call this one "admin", and one has only plain Desktop User access - call this one "user".
2. Log in as user.
3. Go to System > Preferences > Main Menu. Check some items off. In my case, I specifically checked off Applications>Wine and also System>Administration.
4. Log out. Log back in as admin.
5. Install something that adds another entry to the menu. In my case I installed Totem, which is suppose to add the entry Applications > Sound & Video > Movie Player.
6. Log out. Log back in as user.
7. Check the menu. All the items in the third column are GONE!
The current workaround is to go into System > Preferences > Main Menu. Click Revert (confirm it), Close. Log out, log back in. Make any changes that you would like as in #3.