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I also had those problems. Our solution was to rewrite a part 
of the help_class.js file and to change the call to the popup 
window.
The problem is in the javascripts. They work for some 
browsers, but not all. IE 4 is very bad with the help class. IE 
5.0 somewhat better. IE 5.5 and IE 6 are OK.

Regards,
Marlon