It looks like you clear US customs at the Vancouver airport. Is that right?
I was looking at the terminal map. It looks like you check in for your flight, go through security and then go through customs. Those are my guesses.
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I know the air fare to fly back from Vancouver will be a bit more than flying out of Seattle. You would need a few hours to either take a bus or train back and there is some cost to that, plus the added time. Hands down, I fly out of Vancouver. It is also a fairly long flight back to the Midwest, so it is pretty much a full travel day this way as well.