I have what seems a similar problem. I'm using SlimStat, and for a while the human visits and unique IPs shown in the graph were dramatically smaller than those shown in the Summary window on the Visits page; I had no idea which was correct. I tried deactivating and reactivating, with no change. Then I de-installed the plugin and reinstalled. Now the counters show nothing for human visits and new visitors, which can't be right; if nothing else, I'm a human visitor, and it shows my IP address in the IP address box.
Any suggestions? I'm afraid I'm not very code-technical.