gconftool-2 -s /apps/update-notifier/auto_launch -t boolean false

Which according to the description:

The default action (update-manager) will be started automatically.

That should stop it and on mythbuntu probably be the default as they are
typically run keyboard/mouseless so one can't click on anything.

-- 
Update manager flashes on screen before being minimized
https://bugs.launchpad.net/bugs/366968
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