I don't know when it was fixed, but it seems this bug no longer exists:
I can launch Synaptic, and then launch Update Manager, without Update
Manager complaining.
If you still experience the problem, please provide up-to-date steps to
reproduce it. (We no longer show anything in the notification area for
software updates.)
** Changed in: update-manager (Ubuntu)
Status: Triaged => Fix Released
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update-manager shouldn't complain that synaptic is running when there are new
updates
https://bugs.launchpad.net/bugs/43087
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