I can reproduce this use-case in my application. Did you try popup panel's attribute followByScroll=true?
Pavol, not sure, but it sounds like you man you "can't reproduce this use-case in [your] application", is that correct?
I am not able to use pages attached to original post. However, I modified popup panel sample in Metamer in such a way that button opening popup panel is in veeeery long table. When I scroll down to last line of the table and open the popup panel, it is rendered on the top of page, i.e. not visible. You have to scroll to to top to see popup panel.
However, there is a popup panel's attribute followByScroll which was created exactly for this use case. I'm just not sure if that works for peter.boivin