I was wondering if it was related to how easy it is to get money in and out. Bitstamp was usually lower because it was easier to get money out than gox so sellers would accept a slightly lower price in return for better withdrawal service. Then in the boom, buyers moved to bitstamp to get away from gox and pushed the price up. Then in the bust, everyone wanted their money out again, so they sold on bitstamp and pushed the price down compared to gox.

I'm just guessing, though.