I'm constantly hearing people talk about affiliate networks that don't count all your sales. It's pretty easy for an affiliate network to keep some of your commissions and to bill the company for the sales you made. Especially if you don't have a system that keeps track of that.
I don't think there is any particular guideline which you help you distinguish between genuine and scam progs. What you really need to do is, work with the ones which had been around for some time and also before joining some new prog. research for it a little bit.
Personally I like to review the history of the merchant. With some networks (SAS), this can be done to see their average sales/day and their online/offline history. In house affiliate programs I do question and have been burned on in the past Tread cautiously