I’m having similar problems. It started when I updated to WordPress 3.3
As instructed, I turned off plugins before updating WordPress, then reactivated Jetpack (currently at 1.2.2) after WordPress updated.
Now, the Stats only state: “We were unable to get your stats just now. Please try again.”
The site doesn’t get a lot of traffic, but it’s been a couple of weeks and I’m still not showing anything except the above statement.
So, I went to the configure and set it to “Count the page views of registered users who are logged in.” I’ve clicked through a few pages and so far, still nothing except the above statement.