First, remember that it won't work with your Passpack It! button. You need to click on the 
icon in your password list and Passpack will log you in directly to the website. If you don't have an icon like that in your list, you need to set up the basic authentication first. See this article.
Also, you need to make sure that the site you want to log into actually uses HTTP Basic Authentication. Not all sites that use a popup window are basic authentication. If you're not sure, just contact support with the link to the site and we'll try and help you figure it out.
Lastly, if you are sure the site actually uses Basic Authentication, then you need to make sure that you are adding the correct link to your Entry window. It should not be the page on the website that actually pops up the extra popup window.