I think that your pads have a hexagonal shape, this is yet not supported in the PCBMill. You should get warnings about it while the contour is generated. Unknown and not supported aparture shapes are ignored by the software, that's why some pads not translated and not shown at all. If you like to get a correct code from PCBMill, change the pads shape to circle or oval.
Probably later I will add some more apartures, but now I have no time to work on it unfortunately....