Amazon, which I use regularly, has never affected my IE settings or left any unwanted residue on my system apart from the normal one-click ordering method, which proves very convenient when on its site.
Do not think the Amazon website is to blame, but something somewhere is opening up 2 IE windows everytime I start IE. It is driving me nuts.
Tried using pop up defender, but problem with that is, it will not let me open a genuine window, means I have to adjust the " block list" which is just as annoying as having to close the offending window.
you havent said what your normal home page is, its quite common for a lot of pages to come with an extra pop-up. change to google or something as your starting point and see if it stops. Two tools worth using are ad-aware and spybot search and destroy.