I can confirm this. A workaround is to pin the files using synaptic, as
update-manager uses synaptic's pin file (/var/lib/synaptic/preferences)
To pin a file using synaptic, select the package, and go Package > Lock
Version.
** Changed in: update-manager (Ubuntu)
Status: New => Confirmed
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Update-notifier/update-manager and Synaptic does not read package Pin:s from
/etc/apt/preferences
https://bugs.launchpad.net/bugs/125271
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