Thanks for posting Andrew, it was an interesting read, especially the comments part.
Also, I respect the way you left out the company names so that the real issue was the main focus, rather than the post turning into a witch hunt.
Doing the research is necessary to find the top payout. I often have affiliates negotiate/barter payout rates with me for certain offers that are available through other networks, however it's helpful to keep in mind that payout isn't the only factor when choosing which network/program to partner with.
That being said, the huge payout discrepancy that you experienced seems unusually high.