That's exactly right. You'll have the master sabre PNR as that is what our corp TA uses. You'll then have one Amadeus PNR which has the flights with the marketing flight number, the AA one. This won't allow you to select seats. You'll then have a second Amadeus PNR which will most likely only have the one flight on it (but sometimes all of them). This will have the operating flight number and will allow you to select seats.

This is normal and expected behaviour and isn't a problem.

What's even more confusing is that the seat changes won't sync between the Amadeus bookings, let alone to sabre. However, they will stick.