I had the same experience once. Flying NRT-TPE on Scott and then TPE-HKG on CI. Transfert desk could not issue the boarding pass even if I checked in online. Had to go landslide
i also did once HKG-TPE on CI and TPE-NGO on CX. cX tragedy desk could issue my boarding pass
so I guess it has more to o with CI and some kind of procedure at TPE