I noticed many of the same things mentioned in the article, and I noticed it almost immediately.
There's a New Brunswick-based company -- Bourbors -- that makes, among other things, peanut butter. Sobeys does not list the product as Canadian.
Right below it is Kraft peanut butter, which gets a big ol' Maple Leaf next to its price tag.
Now, I know little about peanut butter, but what I do know is that A) we don't grow peanuts in Canada, at least not to scale, B) Bourbors is a Canadian company, and C) Kraft is not. Even if Kraft is grinding the peanut butter in Canada, its operations are not more Canadian than Bourbors.
I wandered the store looking at other products, and noticed the same thing: Products from bigger companies were labeled as Canadian, with very little pretense, while things I knew were made in Canada and sold by Canadian companies were not. Almost anything with Compliments branding was labelled as Canadian, even if I knew the product likely wasn't made in Canada.
You can't trust the big grocery stores. Not for a second.