RichFaces team not able to reproduce that from the beginning. And if you will download and run our rf-showcase sample you will see that panels working in included pages while includes are placed in component-sample.xhtml which uses composition and inherits main application template.
I think I found the solution to my issue. I was using <ui:composition> for all of my pages when in fact I should be using
<ui:decorate>
Per the documentation:
The <ui:decorate> tag provides the same features as the <ui:composition>, but it causes any content surroundig the <ui:decorate> tag to be included in the page, rather than be trimmed, as in the case of <ui:composition>.
I guess IE is very particulate with respect to the generated HTML but by changing to a <ui:decorate> tag, the popupPanel now works as expected.
I run in the same problem here, Firefox is working fine, IE9 absolute rubbish, wrong font sizes and the popups show on the bottom of the page. I found that if there is commented text between the <?xml ... ?> and <!DOCTYPE ... > tag, IE is not rendering the page correctly, Firefox does. This might be an common problem for Netbeans users since the standard xhtml template fits comments between the tags mentioned before.