I go with the "disconnected res systems" theory. I've been comparing AC and CP flights on a regular basis lately, and seen some fairly gross anomolies. One example would be only a few full Y fare CP seats available on a CP operated craft, but lots of highly discounted AC seats on the same plane. I've also seen 0 availability on one, and lots of availability on the other.

There are many variations, but the end results is pretty much like you're looking at two completely different airlines, notwithstanding that they are both selling seats on the same flights.