There is an ongoing discussion in Allan Gardyne's forum about Clickbank merchants.
The gist of it is that ClickBank only track sales by credit card. If someone follows an affiliate link to a Clickbank merchant site, the affiliate will miss out on the commission if the customer makes a purchase using other methods of payment e.g. PayPal, check or money order.
Some merchants are using Clickbank as a free advertising service and avoiding payments to affiliates while others may not be aware that they are wrecking their own affiliate programs unknowingly.
If anyone intends to sell through Clickbank's built-in affiliate programs and wish to offer different payments options in addition to Clickbank, it would be better to explicitly state to your affiliates that they will only be paid for Clickbank sales.
Hope this helps.
All the best,