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[Stefan Pappalardo <stefan.pappalardo@xxxxxx>]

Since lucid has changed the default behavior for the update-manager
there is no Problem anymore with this issue. Please correct me when I
was wrong ;-)

** Changed in: update-manager (Ubuntu)
       Status: Confirmed => Fix Released

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Update manager flashes on screen before being minimized
https://bugs.launchpad.net/bugs/366968
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Status in Mythbuntu, Ubuntu derivative focused upon MythTV: Fix Released
Status in “update-manager” package in Ubuntu: Fix Released

Bug description:
Binary package hint: update-manager

When there are updates in Jaunty (904) and the update manager starts, it shows the update-manager window and shows the window minimizing (with animation).  This can be seen when all other windows have been minimized or when there are no windows in the way of the update-manager window.  This behavior is very distracting and grabs the users attention as it flashes on the screen, the exact thing the "new" notification system is supposed to prevent.

This is just my opinion but maybe a better solution is that when the update manager starts it is in the background but doesn't have its task listed in the panel.  Just like the dialog box that is popped up when downloading/installing things in synaptic (I'm not sure if this is even possible).  Thus making in unable to be minimized only closed, this would also remove it from the ALT-TAB list.  Another alternative might be that the update manager doesn't show up in the task panel until it is minimized, essentially popping open in the background but not visible until you change and/or minimize the window you are working in.

Notes:
1. This is seen when not using a composite desktop, I'm not sure of the behavior when you do run one.
2. The attached video was captured with Xvidcap, I apologize for it not being in Theora but it is viewable with VLC