I have the "Visit not via internal link" condition activated, but the pop-up is not shown when the visit comes from the search engines.
Try this. Search for "papaenapuros.com" in google, and click in my website's homepage (www.papaenapuros.com). Can you see the pop-up? I cannot.
But, if you type the website's address in the location bar directly, you'll see the pop-up.