Yes, removing the appmenu-gtk solved the problem.
Actually, on my current install appmenu-gtk was not installed and the problem didn't exist.
I tried installing it, (just to see if something will happen), and the menus disappeared after logout/login
Then I uninstalled appmenu-gtk, and the menus appeared again.
It seems that the bug is in appmenu-gtk
Yes, removing the appmenu-gtk solved the problem.
Actually, on my current install appmenu-gtk was not installed and the problem didn't exist.
I tried installing it, (just to see if something will happen), and the menus disappeared after logout/login
Then I uninstalled appmenu-gtk, and the menus appeared again.
It seems that the bug is in appmenu-gtk