Looking at the male thread, the thread appears to be incompletely formed. Assuming the female thread is made with a matching tap, I would consider the tooling to be of poor quality. In your post above, the male thread is too small, which confirms what I see. The die must be "mis-shapen" in its' cutting surfaces.
Another posiblity is starting the die almost, but not quite square to the stock. That would account for the mis-shapen threads and slightly undersized finish. This could be determined by running a nut all the way down to the shoulder. If it tightens up as it approaches the shoulder, it indicates a high probability of not starting true.
I nake a practice of single pointing a male thread whenever possible for a couple of passes. Then finishing with a die. It doesn't help much with poor quality tooling, but helps the die run true(r). I also have acquired a contraption for starting a die from the tailstock. I'm not sure if it's truely useful, but I don't do "production" work. The setup time is longer than makin a couple passes with a threading tool.
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