@Alberts

also have that issue on a fresh xenial 64 bits , ext4 partition,
installed from the mini.iso, and using a gnome-shell session with
nvidia-361. This is a pure genuine install (no ppa or else) but share an
ext3 /home with wily 32 bits & an other wily 64-> xenial 64 dist-
upgraded.

1) with the fresh install : when i have 'midori' (example case) and
'synaptic' (other example) opened on  the  same workspace. Then if i
click on the top left x to close 'synaptic', it is closed as expected,
but also the browser (which is not expected). The strangeness: no error
popup nor logged. So its difficult to blame a package or an other.

2) with the dist-upgraded xenial, there is no such problem. But it has
its own home folder (does not share the /home partition.

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https://bugs.launchpad.net/bugs/1538111

Title:
  untraceable serious bug in metacity 3.18

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