I booked this flight using TD points through a company visa. That is potentially why it didn't show up in the system when I first checked in at YVR. But since then, I haven't had issues, so I think once it has been entered once into the system, you shouldn't run into any issues. In the end, I don't think it should matter what visa or system you use as long as your Aeroplan account is setup properly and you use that when checking in online.