Statcounter, sitemeter, google analytics, hitbox, activemeter, wordpress stats and all the others will never agree. Each one of them decides how and what they will count as a hit.
In my experimentation with all of them what I found was that there was absolutely no consistency from one to the other most of the time. One day sitemeter would say there were 100 hits more than statcounter, and activemeter would show 100 less than sitemeter. A few days later they would again play musical chairs. The largest discrepancy I saw was over 200 hits (when the blog I was using for testing was getting only 450 hits per day). I also had a 3 day period where one of them showed hits in the teens (12-19) - not wordpress stats - while the others were still showing up around 400-450.
At the end of a three month testing period on that blog, there was a 26% discrepancy between the lowest and highest totals.
Here's the bottom line: Use any of them only as a general guide to hits. Anything that is not running on the servers your blog is on is going to be suseptible to wild fluctuations since all your hit have to be transferred over the internet to different servers, and there are literally thousands of things that can go wrong between the server your blog is on and the server at the stats place. Next throw in the possibility that the software or hardware at the stats place is screwed up and not recording, or counting things properly.