Numerical Innovations - Help Center

Thanks.  

When viewing the workspace file, there's definitely duplicated drill files.

The drill file you supplied does not have duplicated holes.  So perhaps there was some editing/copy, merging layers; because there's definitely 3 drill hits for every hole.  

I will review the Power/Ground next - however you're using a "negative" layer which is typically not recommended and more difficult to follow for netlist extraction/dfm checks, etc. (in fact negative gerber files have been deprecated in the gerber format).  

To resolve the issue, I would use the command  (menu: Fabrication | Convert Negative Layer...) to convert your ground layers to positive and then perform all checks, etc.  In fact when you send these files out for manufacturing, the fabricator is going to convert your negative layers to a positive layer.   

Everyone from CAM tools to PCB manufacturers' have troubles with Negative metal layers - because they are incomplete.  Here's the direct quote from the Gerber format specifications manual:

Here's a sample PCB manufacturer suggesting to stay away from Negative metal layers,  https://docs.oshpark.com/troubleshooting/inverted-gerbers/

To goal of FAB 3000 is to prevent any troubles with properly manufacturing your PCB designs.  Every board shop in the world will have to manually edit negative layers before manufacturing -- which can introduce unintended consequences  that you may not be aware of (from their editing of your plane layers), until after the boards are made.