What's the point of paying a different price for the same toothpaste at Ralphs vs. Vons? We pay different prices for the same thing from different sellers all the time.

The whole idea of codeshares is that the different marketers can charge whatever prices they want. I'd be more surprised if they always matched up exactly than if they were different.

However, having said that, one reason why the tickets might be of different actual value to you is that the fare rules could be different based on whom you buy the ticket from. But that might also be why you buy from one store over another too, maybe you like the return policy better.