I’m having the same problem. I checked my stats this morning and it was working fine, but after I updated the status plugin to 1.3.6, I’m getting this error message:
If you have just installed the Automattic Stats plugin, this error probably appeared because the API key entered in the plugin belongs to a different WordPress.com user account.
* Have the owner of the API key visit this page and add you to the blog, or
* Get your API key here, then deactivate and activating the plugin and enter your key to add your account to the access list for this blog.
I haven’t changed any settings, just performed the update.