[benjaminRRR]

This is definitely the most likely scenario. Kayak and other aggregating sites have different arrangements with different partners in different regions. In turn those partners have different arrangements either with direct connect or the GDS themselves (who may also have different arrangements depending on the geographic market).

You can get the same effect with other GDS products also, try rental cars for one. The other crazy thing is that different geographic markets are generally responsible for their own revenues, so you can have different promotions, and yield management strategies depending on who is trying to hit their numbers.