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[proteus <1003057@xxxxxxxxxxxxxxxxxx>]

(Continuation from above) Some 15 minutes later, after I finished
writing the above post, I looked again at the system and now I had a
Software Center instance running - and nothing else.

It said it has some updates, so I clicked to start installing them,
before rebooting the machine. When all of the sudden all the windows
appeared again, on all workspaces.

I don't know if this is related to the Software Center (maybe it
restarted something?), the init 3/5 I did earlier, or something else
entirely.

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https://bugs.launchpad.net/bugs/1003057

Title:
  Windows disappear unexpectedly when switching application

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