For now, it seems that the problem is in libdbusmenu (Unity side).
Eclipse is blacklisted in a binary file in libdbusmenu, so the menu is always 
on the application. There is no friendly way to remove it from the blacklist, 
but there is a workaround which involves editing the binary file here: 
https://bugs.launchpad.net/ubuntu/+source/libdbusmenu/+bug/618587/comments/46 
I've reported https://bugs.launchpad.net/ubuntu/+source/libdbusmenu/+bug/890294 
to remove Eclipse from the blacklist, but no one did it so far.
I think the best way to help here is to test the workaround with all menu 
functions and insist on that last bug report I've mentioned, maybe even sending 
a patch for it (I think it should be an one-liner).

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https://bugs.launchpad.net/bugs/613119

Title:
  Eclipse menu does not render correctly in unity bar

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