i was going to post here with a problem with the popups but i just worked it out! i thought i'd tell you what the problem was so that if anyone else was having a problem they could look at this post.

if the page you are running the popup script on has a base target tag then the popup will try to use that rather than the popup script. in other words you can't have a default target and use popups.

hope this helps someone!
ben