I think part of the problem with Canada Customs (especially during the summer months) is that they have students working as customs agents. I find that these people have a harder time detecting "low-risk" travellers than a well-trained professional customs officer. I've never travelled to a foreign country that had students working as customs officers. This explains why Canada is a haven for illegal refugees and human smugglers.

I find that United States customs officers - espeically the older male ones - are most excellent in expediting the process for "low-risk" travellers. This is why I would recommending doing your connection via the US instead of a Canadian gateway city.