The same problem in Linux Mint (Ubuntu derivative).

I think duplicates are showing when the same package exists in two or more 
repos.
Synaptic is combining package with repo so if package exists in two repos then 
the 4 identical packages are displayed (2 repos x 2 packages)...

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https://bugs.launchpad.net/bugs/1533554

Title:
  Duplicate package entries shown when listing by package origin

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