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The best way to circumvent this, is to only use reputable programs, and check the landing page of your affiliate link yourself.
Keep in mind, just because the tracking system is working, doesn't mean the merchant will be honest in reporting/paying your conversions.
BTW, one of the commonly missed merchant tricks/mistakes is affiliate code "leaks." The landing page has your code on some/most of the internal links, but not all.
Also, cookie based systems often the truncate affiliate code once the merchant site has been reached.
btw, froggyman, loved your tracking down of that cat in the spider id forum!