David,
The /frame server does not handle embedded windows properly. The click positions do not take the "offsets" of parent widgets into account, so the clicks are off by the header depth, etc.
I see a couple of options for you:
1) Fix the /frame server. I tried to fix this quite a while back and failed. Perhaps you'll have better luck.
1a) Rig the /frame server client for your specific use. Copy the javascript to your user area and then hard-code the missing offsets as needed.?
2) Build your desired window as a JMRI panel and use the /panel server. It is supported and does a good job of mirroring elements into a live web page. Maybe handle the "scrolling" with a fixed array and "next" "prev" buttons to change the context.....?
3) Build your desired window client-side using javascript and jquery. Using the json websocket server to communicate with JMRI as needed. This would be the most flexible option, but without knowing more about what data you'd need to pass back and forth, this may or not be possible.
?
HTH,
? SteveT