Hi Sergey, OK, I'll see what I can do to simplify the problem. I wanted to mention that I noticed that (for those particular Gerbers) the problem appears on the square pads on all "8" 3M MDR connectors on that board (4 connectors are 20 pin and 4 are 50 pin). It is highly likely that those are the only 8 pads with that "aperture" size. So perhaps it is the aperture table that is being overwritten in that case.
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