Hmmm...very strange. Since Jan this year, I have taken four trips. Each trip originated with a ticket issued in Taipei. The routing would be TPE-HKG-Destination-HKG-TPE. The HKG ports were stopovers, and not transits.
Destinations were Tokyo, Osaka, Paris, and most recently, Shanghai.
On ALL FOUR OF THESE TRIPS, the status points and miles for the THIRD sector (i.e. Destination-HKG) have failed to post automatically to my Cathay account. I have had to submit claims retroactively, and then the status points and miles would appear 3-4 days after submission. For all other sectors, everything has posted within 1-2 days after the flight.