What about the same airline not issuing BPs for a connecting flight?

Last year I was flying CX in F (JNB-HKG-SIN) and the F desk in JNB would not/could not issue a BP for the connecting flight (HKG-SIN).

The connection desk in HKG did take care of me and my checked-in luggage so no problems, but as you could see there are still technological difficulties even when it's the same airline, so it's not a surprise when an alliance still has compatibility issues with BPs.