My blog was hacked just before the 3.1 upgrade. I had to move it to a different subdomain, changed the WP_ prefix in the DB, imported past posts, categories, tags, etc. I changed all passwords and installed the BulletProof WordPress plugin. I have a redirect from my former subdomain to my new one. Somewhere in all this, WordPress Stats quit working.
I went to the WordPress Forums and tried some things that apparently worked for others in the past when this plugin quit. I've tried everything I can think of, including scouring my .htaccess files to make sure Auttomatic isn't being blocked. I uninstalled and reinstalled Wordress Stats. I disabled all other plugins, then re-enabled them one by one. My key doesn't seem to be an issue. I've checked error logs to see if I can spot something. All to no avail.
The LBAK and WP Easy Stats plugins both work, but I like WordPress.com Stats best. I hope something can be done by the author or some information about what more to check can be made available.