"Okay, I'll buy that...but what causes the process to happen? Is it slight inaccuracies in gene transfer at meiosis?"
Several:
1. Primarily, mistakes in DNA replication (for animals and plants this has to be in the germ cell line). If you are not familiar read the history of hemophilia in the royal households of Europe, all began by a mutation in one of Victoria's eggs.
2. Natural mutagenic things - cosmic rays, chemicals like polyaromatics, mutagens in your food, radiation, UV light, etc. (I know these are mutagens, but they still are "natural").
Also...what does it take to get a population of animals that are cross-fertile with one another, but no longer cross-fertile with other descendants from their ancestral line?
Physical separation for one, but I will have to defer to others for other answers.
I would think Victoria was a bit young to be responsible for the hemophilia in the Romanovs...but of course I could be wrong.
More to the point, hemophilia isn't a useful adaptation. It doesn't contribute to survival. (I know that you weren't claiming it was; you were making another, quite valid point.) All of the mutations I've ever heard of in humans are actually detriments to survival, causing conditions like cystic fibrosis, hemophilia, beta thalassemia, or Down syndrome. When was the last positive, advantageous mutation in humans? Shouldn't there have been one in recorded history?
If Asperger syndrome turns out to be due to genetic causes, and it probably will, that may be our one. Geekdom is a survival advantage. It may, however, give up in reproductive success what it gains in survival. =]