Thanks for this addtiional information.

Can you please run:
$ /usr/lib/update-notifier/apt-chk  ; echo ""
and attach the result here in a situation when update-manager has updates, but 
no icon shows up?

Can you please please run:
$ ps ax |grep update-notifier

and check if you have a "notification area" applet in your panel.

thanks,
 Michael

** Changed in: update-notifier (Ubuntu)
Sourcepackagename: update-manager => update-notifier

-- 
update-manager doesn't detect updates available
https://launchpad.net/bugs/94078

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