I actually do empirical work and I use a whole bunch of different indices to do this. The one Scott refers to is an industry-based one, which is quite opaque in its methodology. It doesn't meet academic standards, but it doesn't mean it's useless. It's based on what industry, especially multinationals, want. It's useful from that point of view, but I wouldn't take it as being the ultimate ranking. On the other indices, Canada does considerably better.
The more important point is that while Scott mentioned there's a correlation and these two numbers go together, except that in the case of Canada there's no causation. It's like saying how much snow we get in winter goes to your IQ. These two things may or may not be correlated, but it doesn't mean they're causally linked, so take this with a grain of sand. It's a useful piece of information, but don't rely on it too much. Look at the underlying economic analysis, which says that Canadian IP is not driving Canadian innovation; it's U.S. and European IP that's driving Canadian innovation.
How to get Canadians to access that is the more interesting figure, and none of these rankings take that into account.