Are you sure this not the long-standing issue with domestic continuation flights of international flights? These, along with JFK-SEA/PDX/DEN/LAS/SAN/PHX and flights to Caribbean/Mexico/Central America, all show as ineligible for F upgrades prior to booking due to carrying J/C/I/D/Z fare codes for F. Once you have booked them, they will correctly show as eligible.
Probably this, thank you. Though in this case the domestic flight number continues into a TATL flight.