Further inspection reveals the following is happening:

Unity redecorates window (at some point, does not matter)
Mutter marks the window as "redecorating" in mutter-window.c
Mutter never unmarks the window as "redecorated", thus causing effects to never 
be triggered on events
No event trigger results in no window mapping

The attached patch fixes the issue

** Patch added: "mutter.patch"
   
https://bugs.edge.launchpad.net/ubuntu/+source/unity/+bug/620758/+attachment/1519810/+files/mutter.patch

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Applications don't always show up when unminimizing
https://bugs.launchpad.net/bugs/620758
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