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

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https://bugs.launchpad.net/bugs/618557

Title:
  Missing menubars in at least two wxWidgets applications: boinc and
  truecrypt

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