I posted earlier about why joining several different affiliate networks is recommended. One commenter mentioned that if you do that you'll sometimes see the same merchant using different networks, and that the size of the commissions they pay for leads or sales varies between each. Obviously, you should go for the one with the highest payout.
I've done that recently with one program. It's just a pay per lead one. The commission is around three bucks per lead at one network, but over double that amount at another. I'm glad I've done this, and wish I had switched over earlier. This is a popular program and if it keeps on going for a long while I'll be making hundreds of dollars more per year from it.
That said, I can't be sure when this higher commission commenced with that particular network. I think it might have only started recently. In any case, it is a compelling reason to not only join different networks, but also to keep browsing through what they offer occasionally. Do that and you're sure to find programs that will bring you more money for the traffic that you're already getting.
As to why merchants vary their commissions between networks, I'm pretty much in the dark. Maybe it reflects the relative quality of the signups that the affiliates from each program deliver. Or perhaps the setting of commission size is partly out of the merchant's hands, and is recommended by the network? Or it could merely be due to a lack of organization on the merchant's part ...
I really don't know the answer. But for anyone who promotes affiliate programs it's certainly a factor worthy of close consideration.