"If these are always absolute barriers to reproduction, there is a problem."
Let's say you had an insect whose chromosomes got "stuck". It produced 1000 eggs. All of a sudden you would have a new species with a thousand individuals.
Look, I'm not a creationist pulling your chain. Most of the species that inflame the debate are mammals. The question is, how does the shift in chromosome count occur, and does it prevent cross mating. I have seen suggestions that humans and chimps could probably mate, despite differing chromosome count.
There are quite a few humans with anomolous chromosome counts, not all of which are retarded or sterile.