Thanks for posting this!
Skimlinks is a company we've been working with for about a year. Basically when someone on BYC links to Amazon, eBay, etc., the Skimlinks system adds a "referral / affiliate code" to the link so any purchases made at those sites kick a few pennies back to BYC. It shouldn't impact the purchase experience and definitely doesn't impact the price, etc. of the items.
I'll look into why they are doing the popup... it might just be a legality thing for some users or links or something.
Also, we're looking into ways of bypassing skimlinks completely to avoid this altogether.