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[Cefn <launchpad.net@xxxxxxxx>]

With more investigation, this seems to be exclusive to Synaptic package
manager. Is it possible that Synaptic intervene in window ordering in
some non-compliant way to create this issue.

I seem to recall that the Ubuntu "update manager" messed around with
window orderings (where you had to close it to stop it blocking your
view - you couldn't foreground other windows over it). Perhaps they both
have similar behavioural problems. I'll try raising a bug against
Synaptic.

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https://bugs.launchpad.net/bugs/1166262

Title:
  Compiz Window Decoration handler not bound to foreground window

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