This is why:
http://plugins.trac.wordpress.org/browser/stats/tags/1.7.2/stats.php#L685
The deactivation hook deletes your database information. I’m guessing you’re manually deactivating the plugin, updating, and then re-activating? If so, that runs the deactivation hook. Fortunately, that’s not from the latest version. This is:
http://plugins.trac.wordpress.org/browser/stats/tags/1.7.3/stats.php#L686
So that shouldn’t happen anymore.
By the way, you shouldn’t think that this means you were doing anything wrong. They shouldn’t be deleting information on deactivation, only on uninstall. Kind of strange that they were doing it at all…