I'm experiencing the same situation. I have a revenue economy ticket issued by CX, EU-DOH-HKG-NRT. All my flights are CX codes, EU-DOH-HKG are on QR metal. I have OW Sapphire (BA Silver), both online and the help desk can select extra legroom seats, but the same situation, after a few hours my seats are unassigned, except the sector on the standard seat and on CX metal.
QR agent said that extra legroom seats are chargeable and it gets unassigned as no payment was made, but I argued that as OWS member I should be eligible to select those seats free of charge. Then he insists that BA Silver is equivalent to QR Silver which is OW ruby...Then I asked him why I was allowed in the Gold Lounge at DOH. He answered that for lounge access BA silver is considered to be OW Sapphire, but QR flight BA Silver is considered as QR Silver OW Ruby. I think this is total nonsense. I assume there is a glitch in the system when it comes to seat selection for OW status holders with non-157 stock tickets. Has anyone managed to keep the assigned seats or at least managed to select those seats at the online check-in stage?