Hi Catherine,
Don't worry about pop-ups or any other details between your affiliate links and the purchase, all that is required for us to track a referral are two things:
1 - The buyer clicked through an affiliate link recently (six months by default, a year with the settings you wish to apply), which places a cookie in their browser.
2 - The buyer purchases from your E-junkie account from the browser with that cookie file.
As long as that cookie is there we can track the sale, so it is perfectly fine if someone visits your site but does not purchase for a few months.
