In 2004, Fox Video released the first 5 episodes of BM on DVD. I think that's the one you saw at Zellers. It's usually listed between 10 to 15$.
In early 2006, Rhino Video released the complete series (Season 1&2 = 26 episodes). That one is a little harder to come by, and not available in Quebec stores.
This new one is from Sony is set to release next week. I agree that this is probably not the full season, but would they again release the pilot? And if Sony is starting to release Transformers, why start with Beast Machines?
I could not find the item on the US Amazon. Could this be a Canadian only release? Or a misprint?