Nevermind it worked if I remapped the mouse with xinput. I discovered
that the middle button actually was recognized, but it wasn't showing as
button 2 as expected but 6.

1. The command "xev | grep button", gave me the button 6 if I clicked in the 
xev window with the middle button.
Then I had to remap the mouse buttons from 6 to 2 (2 is the middle button):
2. The command "xinput get-button-map 8" was giving me my buttons "1 2 3 4 5 6 
7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24"
Then I remapped them:
3. "xinput set-button-map 8 1 2 3 4 5 2 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
21 22 23 24", the sequence remapped my sixth button to number 2, the middle 
click was after that working.

To get it loaded each time I start Unity I autostarted that last command
at login.

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https://bugs.launchpad.net/bugs/1581088

Title:
  Middle mouse (wheel-click) button stopped working after upgrade to
  16.04

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