Since Post Affiliate Pro version 5.4.27.4 we have added option to generate click commission for unique clicks only. It's located directly in click commission settings of your campaign.
If you are using older version of Post Affiliate Pro software there is a workaround to achieve basically the same functionality. You will have to set up a fraud protection against repeating clicks in your Merchant panel->Configuration->Fraud Protection->Clicks tab, just like in the image below.