Just my observation but both Synaptic and the update manager should be in sync 
as far as whatever updates are available. I have seen this same type of issue 
plague openSuSE. The update manager should be an extension  of synaptic, not a 
separate package management component which conflicts. Are they linked? Do they 
communicate and share update info?
Just a thought.

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[hardy] Update Manager and Synaptic fail to install recommended updates without 
any explanation
https://bugs.launchpad.net/bugs/227282
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