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During netlist comparison I keep gettings warnings "Missing External Net" on unattached pads. Is this a short?

The warning "Missing External Net" is not a short (or a necessarily problem).   What it's saying is that the IPC netlist generated from your CAD did not consider "single pads - without any connection" as a valid net, so those pads were not included in the IPC netlist.  When you extracted a netlist (using FAB 3000), you must have checked the option "Allow Single Point Nets"; this has led FAB 3000 to believe that you do want "single pads - without any connection" to be considered as individual nets.  So the warnings from FAB 3000 are simply stating that nets (from the single pads - without any connection) exists in the database, but they don't exist on the IPC file.

To prevent those errors try unchecking the option: "Allow Single Point Nets" when you run netlist extraction (menu: Tools | Nets | Netlist Extraction...), and then proceed with netlist compare.
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