Hi David,
If the Fills Out Form trigger is working for your program level tracking, go to the activity log of one of the leads who filled out the form, and check to see what landing page was recorded.
I have not studied the new embed code, but with Forms 1.0, part of the process of embedding was replacing the "LPID" in the hidden form parameters. The LPID is an identification number for a particular Marketo LP. When submitting a form, the LPID and FormID are included in the submit, telling Marketo which form on which LP was filled out. When embedding, you are putting the form onto a NON-marketo page (typically) so there shouldn't be an LPID. In the case you describe above, it sounds like by using the embed code, the LPID is probably being stripped out, even though you are then embedding it on a Marketo LP.
I'll bet you could get around this by determining the LPID of your landing page, and modifying the embed code, but probably best to have an HTML expert who knows Marketo handle it. If you don't have such a person, let me know and perhaps my company can help (we're a marketo services partner).
Thanks!