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.
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.