I think I have a workaround for this. I noticed that:

gconf:/apps/update-notifier/regular_auto_launch_interval = 7

and amended this to 1. Now update manager pops up every day. This is
probably inelegant (i.e bash update manager with a hammer kind of), but
at least I'm seeing updates!

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Update manager not showing notification of daily updates
https://bugs.launchpad.net/bugs/549217
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