I'm not the OP, but I also had that problem recently, and, yes, those flights did show up in my account online. in fact, as I said, those are actually in the same booking - e.g. TPE-HKG-SYD, checked in at the same time, CX MPO # showed on both boarding passes, but only TPE-HKG got posted and HKG-SYD didn't. it happened more than a couple of times already recently I think.

on your problem - i.e. TA entering the MPO # and yet bookings didn't appear online, I had this problem very frequently the past few months too. My agent (Swire Travel) couldn't figure out the reason at all. The only way for me to solve it (somewhat manually) is to call MPO myself and ask them to re-enter the MPO #, then it'll show up online...I still don't know the reason so far though. in my cases, it's most often just pure KA or pure CX bookings, not mixed bookings.