I found out what the problem was.

Somehow the appmenu packages for gtk applications had been removed (I
didn't do it manually). I reinstalled them and it seems to have fixed
the problem.

** Changed in: indicator-appmenu (Ubuntu)
       Status: New => Incomplete

** Changed in: indicator-appmenu (Ubuntu)
       Status: Incomplete => Invalid

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https://bugs.launchpad.net/bugs/1106487

Title:
  Some applications not using the global menu in 13.04 (using default
  settings, none of them have it disabled)

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