Pop-up blockers, for a while, caused some major problems. It used to be that they would block any pop-up, even after clicking on a link (so many people had to shift-click in order to get the new window).
Some pop-up blockers still do block all pop-ups. So technically, if you want the best chance of getting the referral, you could consider using the same window. But I found that, for the most part, if you used “_blank” in your HTML to open a new window, it would work properly. The pop-ups that failed the most often were inevitably caused by javascript links.