Sorry if I was unclear, but I'd like to see some of the example requests and responses where you're observing this behavior, rather than just a description.
Possibly a silly question, but when making a request for a new page, are you passing the value of "nextPageToken" from the previous response into the new request?
Scripting it is a bit unnecessary. You can edit the markup of your embed code directly, so long as you don't change the id:<form id="mktoForm_621" yourAttribute="your value"></form...
>I can't seem to page through the results (they return a maximum of 200)Paging is done through the 'offset' parameter>Filtering via Folder only returns the immediate child results,...