You are right TaxDude.

I called AC again and got someone who knew what she was doing. She said the flightpass causes the system to hang up as it tries to make the second flight (for me the YYC-LHR one) to look like it happened last year. She knew what to do and then stayed on the line while I checked us in. She confirmed that we are still on the waitlist.

Of course, while I was doing all that checking in I think I mistakenly put the wrong year down for my passport expiry so I will likely pop by the airport tomorrow morning to make sure that is ok, at which time I can reconfirm that we are on a waitlist. We only have 45 minutes in YYC so we won't have any time there to talk to the gate agents about upgrades.

Thanks for the advice.