Yes, just a regular ol' Marriott.
I've been thinking about this and came up with a theory:
My "qualifying" reservations were LNF'ed. I'll bet the LNF process makes the booking appear as if it was booked by phone, rather than online (a requirement of the bonus offer). Then, the AMEX bonus system ignores the charge and throws-out a generic error. And, the AMEX chat team then makes-up a BS reason why the bookings don't qualify.
I'm not sure if it makes it looked as if it was booked
by phone, but yes, I bet it is indeed because
your reservation was modified (by someone else) after booking. It may have simply thought the reservation was booked by "the LNF team" (a booking method qualifying for elite benefits by Marriott, but not a booking method qualifying for this Amex promo).
And I bring that up because I've heard of other situations where a booking someone made online (or using an app) somewhere (I can't remember in which hotel program) didn't get acknowledged as a reservation booked online because the hotel upgraded the guest, and from that point the system only had a record of the hotel modifying the reservation, no longer the original info of how it was booked.
So anytime you make a reservation and the reservation is modified by someone else (for whatever reason), that may risk promos which require the original booking method be recognized, depending on whether that system "preserves" your original booking method when the reservation is modified.