There are good programs and there are bad ones.
- Good programs track your sales accurately, pay you on time, have a decent number of return days, offer performance incentives, hire affiliate managers who do their job well, don't engage in shady business practices, have a site which converts well to begin with and sell only their own products on their landing pages.
- Bad programs underreport sales and overreport reversals, run their business in unethical ways, have affiliate managers who are impossible to reach, don't pay on time, run 3rd party ads which will make money for THEM but won't count as sales for you (i.e. running adsense on their landing pages)... just to name a few.