Were you using focus-follows-mouse or click-to-focus at the time? If
the former, it could be that the progress dialog kept focus due to mouse
placement. I have that happen fairly regularly.
This could also be considered a duplicate of bug 215126 which asks that
the everything-is-modal method currently employed by update-manager be
done away with for usability reasons...one of the listed ones being this
situation.
** Changed in: update-manager (Ubuntu)
Status: New => Incomplete
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Upgrade error popup was placed behind main window
https://bugs.launchpad.net/bugs/165161
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