The problem persists in 7.10
What is strange is that I have a package pinned in synaptic, but if I press 
mark all upgrades then that specific package is selected for upgrade.

Anyway, I think that all comes from the fact that there is no single way to pin 
packages in a ubuntu system (synaptic update_manager apt use different 
backends).
If you agree I would suggest to mark this bug a duplicate of 
https://bugs.launchpad.net/ubuntu/+source/synaptic/+bug/42178
and file a bug to ask for use of the apt pinning method for all the 
applications.

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update manager doesn't honor (eg. synaptic) pinned packages
https://bugs.launchpad.net/bugs/84176
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