I had the same problem. I discovered that if I deactivate JetPack and then reactivate it and walk through the steps of authorizing it with WordPress.com then it works fine.
Thanks @jondavis. It worked great. Now I would just like to get the session to be shared so logging into one also logs into the other.
It is including a few more posts, but the numbers are still wrong. I guess I will try a different stats system. Can anyone recommend one that works or can at least be troubleshoot?
