JabRef version JabRef build from master 21.07.2016 on Ubuntu 14.04 and on Windows 8
Steps to reproduce:
When I...
Have you checked the groups preferences? There may be some combinations there which causes the problem.
I just saw that this is an option you can set in the preferences:

So not really a bug, only a questionable option IMHO.
I would simplify this by removing these two options and either the group window is shown, or it isn't, depending on the group toggle status.
Most helpful comment
I would simplify this by removing these two options and either the group window is shown, or it isn't, depending on the group toggle status.