I am getting hundreds of shorts when I run Netlist Compare on my Gerbers - however if I import an ODB++ and run Netlist Compare there are NO shorts (on the exact same design) - Why?

Typically when there are so many shorts, etc. - indicates something was incorrectly setup, usually (the drill for Blind/Buried) or wrong layer type assigned.

When I view your sample FAB 3000 workspace file (*.wrk) it has not been setup correctly for Blind/Buried drill.   When I import your ODB++ the Blind/Buried drill is correctly assigned -- that's the different between the ODB++ and Gerber -- with Gerber you need to assign layer types, stackup order, drill blind/buried, etc. 

Here's some examples how to setup Blind/Buried drills, 

https://support.numericalinnovations.com/support/discussions/topics/14000002802 

If you do not assign the Blind/Buried drills they will be treated as THRU-HOLE which is why you received so many shorts.  

By simply assigning the Blind/Buried Drill I get the "exact sample results as the ODB++".