Which ship are you on in September? My husband and I are cruising Vancouver round trip on the "Summit" on 9/10/04. If you get stuck with taking the bus I would love to hear how it turned out for you.
I have taken that bus the opposite direction last May from Vancouver to Seattle. It took almost 5 hours and you have to stop at the border and they take all the luggage off the bus for the security inspection and you have to go through security again and all your carry ons. Actually, that whole process went fairly quickly and smoothly.
Though the scenery was beautiful in spots on the bus ride, it was tiring. That is the problem booking your airfare through the cruise line you don't have any say in what you get and a lot of the Alaska cruises bus people to/from Seattle. The airfare is much cheaper to Seattle than Vancouver. That's probably why they do it.
My travel agent told me you can take a taxi from the Vancouver airport to the ship terminal for $20.00 so that is what we are doing. Much cheaper than the transfers.
The only benefit in booking through the cruise line is that they will hold the ship for you if your flight and transfer is making you late to catch the ship only if booked through them.
They won't do that if you booked it on your own. If you miss the ship, it is your dime to try and catch it at the next port.
Well, sounds like this is one of those learning lessons things. Sure do hope it works out for you and they will change it, but don't bet on it. I've heard all the cruise lines don't have much compassion in this type of thing.
Just remember though that you will have a great time once you get on the ship. Alaska is one of the most beautiful places to cruise. We cruised Alaska in May, 2001. I could go every year.
Have a great time. Please write and let me know how it goes.