Come to think of it, I had same issue checking in at BKK for a JL flight to HND (reward). Spent 1.5 hours at the check in counter checking in. Agent had me get seated at the counter - while the JL agent at BKK worked with AA.

Issue is really Sabre versus Amadeus.

Sabre keeps old ticket numbers in PNR. Apparently Amadeus can't work with old ticket - new tickets don't get associated.
So who needs to fix?

AA when they reissue ticket, if the could, create a new PNR as well as ticket then only one ticket number in the new PNR.
Amadeus needs updated to select the latest ticket number.

Each are pointing to the other.