The problem is, that you want to place the replicated site in the same directory as in which the Post Affiliate Pro 4 (PAP4) is installed.
In general you should use another url for your replicated site than the URL of your PAP4 installation, then it should work correctly.
Example: imagine you have installed PAP 4 under the following URL: www.yourdomain.com/affiliate_program
It is correct, if the replicated site is under the following URL: www.yourdomain.com/<affiliateID> or www.yourdomain.com/anything/<affiliateID>
It is not correct, if you try to use for the site replication the following URL: www.yourdomain.com/affiliate_program/<affiliateID>