What type of site are you starting an affiliate program for? If you are going to be running any sort of a substantial program that is turning decent revenue with a fair number of affiliates, I would be nervous about integrating a "$99 script" to manage everything.
This could be setting yourself up for many headaches in the future if the script malfunctions or goes haywire. I guess it really depends what you are selling though. Is it for a poker site?
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