I fly CX in E a lot and never had problems...maybe it's the new 9 digit IB# that CX can't handle and mis-comms with IB. You booked directly with CX with Cx flight numbers?

Btw what were the fare class for the short hauls? Was there PE or were you in H?

Btw FUK-HKG is under 1500mi, so get 90/75 EP Vs 175/150 for TYO, better lounges too...