Had a similar experience a few months ago trying to book BOS-JFK-EDI with Mint on the second leg only (no Mint BOS-JFK).
JetBlue . Com couldn’t manage the connection. I assumed the mix of Mint and economy seating threw it off. Separate legs it could book.
Ultimately , I booked DL direct BOS-EDI-BOS mostly because B6 couldn’t figure it out.
Anyway, no solution for you. Mostly affirmation that you are not the only one.
Mike