I've noticed this a few time as well, and not just with fertility but the other genes too. I bought an animal yesterday where I'm sure every gene was between 50 and 70%...and once it got into the enclosure they were all red, way lower than 50%.
This weird change is something I've seen at least a half dozen times but I've always assumed I was just a dork and somehow bought a different animal than I thought I did. Seeing you say the same happens to you, I'm starting to question that thought.