I'm running Ubuntu 12.10 with Unity 6.6.0, and I have faced this problem
as well. I can confirm that I was too running a virtual machine, when
this happened. Specifically, I was running a Ubuntu 12.04 VirtualBox
image (set to not exclusively capture keyboard and mouse). One behavior
I noticed was that tapping the Super or Alt key would open up both the
host's and guest's Dash or HUD, respectively. This is somewhat expected,
I guess, but sometimes annoying.

I did not notice exactly when the host's HUD became permanently visible,
but it has stayed there even after I closed the VM. Attached screenshot
shows that the HUD is as if painted on the screen, but not really alive,
i.e. I cannot type anything into or close it by tapping Alt (strangely,
the cursor even blinks sometimes). Elements from other windows (in this
case a terminal) get drawn on top of the HUD, and then sometimes the HUD
gets drawn on top (typically when the other window loses focus).

I haven't experienced any such problem with the Dash.

** Attachment added: "Screenshot showing HUD refusing to disappear"
   
https://bugs.launchpad.net/ubuntu/+source/unity/+bug/1036873/+attachment/3362390/+files/screenshot_HUD-stuck_2012-10-01_14-03-02.png

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https://bugs.launchpad.net/bugs/1036873

Title:
  HUD/Dash refuses to close

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