Welcome to the world of closed-source software. There are many reasons that people like open-source, but one of the big ones is that if you're having this problem with it, that just means that you're lazy.

I recognize that not everything is open-sourceable. Google is a good example, though I'm surprised that they don't document their PDF-scanning stuff better. But if you had the source code to Webalizer, you could just see exactly what it's doing, and change it if you didn't like the way it was doing it.