Not true.

I was recently able to OLCI on CX flights issued on BA 125 stock and AA 001 stock. This was after CX migrated to Amadeus Altea Customer Management System ("Altea CMS") for check-in at all ports.

The only time OLCI seems to fail [false warning that e-ticket number is not found] is when a pax is originating from a port other than HKG (eg. BKK, MNL, SGN, BOM etc.) and has a subsequent connecting flight from HKG.

The online check-in system (when pax attempts to do online check in for AAA-HKG-XXX) seems to think that it does not have "control" of the e-ticket coupon (especially when it is issued by another carrier) for the subsequent HKG-XXX flight.

To the OP, was your ticket issued before mid to late November 2014 (before HKG migrated their check-in system to Altea CMS [while other Asian ports were already migrated])? If so, there is a possibility that the "control" of the HKG-XXX e-ticket coupon might still be with CX's old check-in system (CUPAC) and might not have been reassigned to Altea CMS! However, when checking in at the counter, the agent can always pull up the e-ticket image and gain control of the HKG-XXX coupon to allow for check-in to occur.

Note: Even if you are unsuccessful at OLCI, by the virtue of having tried to initiate a check-in session, SEC numbers will still be assigned based on the time you attempted check-in. You can still get a low SEC number if you attempt check-in once open even if the transaction is unsuccessful.