Welcome to the FAQ website covering document topics in Canada.
Since the ETA was released I cannot check in online and the checkin staff at the airport find it very difficult too. What do I need to do to get the “system” to recognise that I don’t need an ETA and that I do have a PR card
You should try contacting IRCC and the CBSA to try to resolve the matter. There could be confusion regarding your name or regarding something else.