I recently installed a short link software YOURLS, and I finally got the proof that WP-Stats is not counting visits properly. I published post on the website, got the short link url and tweeted the link.
In the next two hours, YOURLS logged 20 hits. And WP Stats logged only 2. I have added some additional logging for referrers and from 20 hits logged by YOURLS only 3 were from search engines, so most of the hits were not registered by WP-Stats. Google Analytics has logged 17 hits in that period, excluding the search engines.
Second problem is that WP-Stats is not logging direct visits to custom taxonomies pages. Other visits tracking solutions (like Google Analytics) were counting visits to those pages, and they have a rather heavy traffic because I use them as a fully qualified pages with generated content.
In terms, Google Analytics has logged 70% more page views than WP-Stats in the same period. I use WP-Stats mostly for quick facts stats, but such discrepancies makes WP-Stats really unreliable and not to be trusted.
Why the WP-Stats report so different counts from other similar systems?