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I having some difficulty getting correct netlist compare results. Either the IPC356A import or the extracted netlist is giving me compare shorts.

In many cases, PCB CAD packages output IPC356A data that does not line-up with the gerbers (this is due to the CAD softwares' output process where it may use different origins when exporting different data types -- I don't know why they do this but it's very common), so after importing the IPC netlist, please verify that is aligns up to your gerbers. If not goto menu:  View | External Nets | Offset... 

Once your External IPC356A netlist aligns up with the gerbers, you should get the results you're looking for when running "Compare Nets".

Here's another similar link with a movie tutorial:
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