I'm very new to all this, have not even "opened" my web store yet or setup e-junkie. I've set it up with paypal, but that's as far as I have gotten. Anyway, I might have some useful input on the problem you are describing.
My site uses Lightbox to generate a nice pop-up enlarged picture of the product. This uses java script. The E-junkie demo seems to have the same visual effect. In testing my site I've noticed, especially with IE, if the user has java disabled or does not allow it via the IE security warning pop up bar at the top of the page, the default action is my enlarged image will open in a new window as opposed to the Lightbox popup. This also seems to happen with certain browser security settings in the "paranoid" range, even if java is enabled. And it really is IE specific. Firefox and Opera have not done this once as far as I know.
This isn't exactly an answer to your problem, but maybe it is an angle to check on.
edit: I forgot to mention, depending on the users settings, they may not even get a warning. It (IE) will silently disallow scripts, thus breaking the pop-up effect.