Sam L.: I have separate sections for PPAs, and it work separately for each one, 
so I can select/deselect all updates from elementaryart PPA, but leave the 
other PPAs updates selected, as they are by default. I have attached a 
screenshot showing 4 separate PPAs, and I have manually deselected 3 of them, 
by clicking their section headers. If this does solve the problem for you, then 
I will mark this bug as a duplicate of bug #603974, the bug for which the 
section checkboxes have been implemented.
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** Attachment added: "screenshot of deselected section checkboxes"
   
https://bugs.launchpad.net/ubuntu/+source/update-manager/+bug/745393/+attachment/2234153/+files/sectionchecks2.png

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Title:
  Option to deselect all  packages on a "per-program basis" would be
  helpful

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