I had the same problem (with both Unity and Ubuntu Classic), on a fully
up to date Natty install. I found that the setting that was causing the
problem was in CompizConfig Settings Manager, Workarounds -> Keep
previews of minimized windows, which I had enabled in part of my vain
attempt to actually have some kind of reasonable tab switching that
included minimized windows. Disabling this setting makes the windows now
minimize without having the invisibility problem, so the workaround
implementation is obviously broken.

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https://bugs.launchpad.net/bugs/754065

Title:
  Minimized windows are invisible but present; minimize COMPLETELY
  BROKEN

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