I have the same issue (fresh install, new home dir). Affected applications: 
nautilus, gedit, eclipse. I have found the following workaround to restore 
menus for current session:
* delete ~/.cache/compizconfig-1
* relogin
... and all will be ok until the next reboot.

It looks like this bug occurs after update  *.db files in
~/.cache/compizconfig-1 directory

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https://bugs.launchpad.net/bugs/1532226

Title:
  A significant number of fresh boots or restarts result in no menus for
  most apps

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