You know I was close to telling you a ridiculously long story, but while writing, I had figured the reason, and feel immensely thick for not thinking this sooner.
All the ones that have the mark, were traded. I can only assume that before I received it they got pokerus with a previous trainer, and were cured. I strongly think you're right, things tend to go over my head. Well... I'm dumb, actually, that's me normally.