After downgrading to unity 5.10.0-0ubuntu6, I don't have this problem.

With 5.12-0ubuntu1, I had the problem as described - after closing and
restarting GIMP once, it no longer appeared in the launcher or in
ALT+TAB.  Switching to it required closing/minimising all windows in
front of it.

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https://bugs.launchpad.net/bugs/995916

Title:
  No launcher icon for Gimp windows

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