GND fill polygon not connecting to GND pads

[engineeringNCMXB]

I am not sure why a ground fill polygon is not making a connection to pads. 

The net names have been verified. When I select the airwire, everything highlights. I have tried with/without thermals. There are no keepouts (that I know of). On the footprint, I checked every available layer individually looking for a culprit. 

I am not sure what else to check. 

[engineeringNCMXB]

....problem found......

This design is linked to Fusion 360. I had reference holes in the PCB outline so that I could properly place the USB connector. Eagle sees the holes and obviously does not fill with copper. 

When the hole were removed in F360 - the polygon filled as expected. Kinda sneaky thing, but good to know.