I think I understood what you mean.
To avoid such problems, see here a solution:
http://bobby.watchfire.com/bobby/html/en/gls/g269.html
Also have a look at a page I build with a pop-up windows, which functions even if the user have disabled JavaScript in his browser:
http://www.webnauts.net/popup.html
If you have any further questions, please feel free to post!