I have had slight puffiness in that area. If it goes away, I'm not too worried about it. A lot of people have weight gain after long rides, so that may just be a place where the weight gain manifests itself in a noticeable way. It's worth experimenting with different shorts.

Going to see the doctor for a checkup and not having anything wrong is not necessarily an indication that nothing is wrong. They are doing triage for the most likely things that will kill you, not giving you a clean bill of health. OTOH, they would be stumped by this one, I'm almost positive about that.