I have also run into this problem, in my case I do not even recall who the issuing
carrier was, but I was leaving TPE on UA to NRT, and connecting to AC to YVR/YYZ.
I had changed the date from the previous day, and the routing had changed from
TPE-NRT-YYZ since the non-stop was not running that day. I spent 50 minutes at
the check-in counter while UA and AC's local agent battled this out on the phone,
despite my having emailed confirmations, including ticket numbers.

For paper tickets, I still carry the small endorsement stickers, which, having called
the airline to confirm changes, i would then sticker myself.