I can confirm this bug (again) in Ubuntu 16.04 too with all updates
installed.
** Also affects: nautilus (Ubuntu)
Importance: Undecided
Status: New
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Super key works only for default input layout. When you go to Settings
-> Region and Language -> Input sources, the super key will work only
for first input layout. When you change position of them the bug with
super key switch to second layouts and vice versa.
Possibly could be related to this
