I tried to call my old customs broker to get his take on this but he is out of the office this week. Have you used Norman Jensen before as they are typically very good and they deal with canada -
www.ngjensen.com/
I would be going berzerk at my agent for not straightening this out. When you brought the goods into Canada did they not force you to show the original bill of ladening into the U.S.? Did you import the goods into Canada as having come from Taiwan? Do you have any info concerning the origins of the goods or anything identifable?
Also, the tariffs for goods are not the same from Taiwan to Canada and from Taiwan to the US as I used to have to do different customer price books because of this. I can see customs wondering if something funny was going on with the original to avoid tariff.