Data point but whenever I fly YYC-YYZ-DTW, I have the same issues above on check in, or almost anything else I try to do. I have now allotted 10-20 min just to go to the desk (at near midnight, mind you) just to get boarding passes in hand (as opposed to PDF for my first flight) for my flights. I generally am able to get both BP's though. I don't recall a time when I didn't have that.

This is obviously a DL connection.