Forwarded from: https://bugs.launchpad.net/ubuntu/+source/xfwm4/+bug/335928
"For Ubuntu 9.04, update-notifier behavior was changed such that update-manager will be automatically launched on a regular basis, but behind other applications.
It does this by launching "update-manager --no-focus-on-map". On standard Ubuntu (using metacity), this behavior works properly.
You can manually verify by running that command in a terminal.
On Xubuntu & Mythbuntu (using xfwm4), the update manager window pops up above your running application."
Yeap, true, yet another focus stealing prevention issue.
Should be fixed in trunk with rev. 29657. Please test against trunk and reopen if the problem persists.