I had this problem too. I fixed it by adding the email address for my service account to the Google Analytics profile I wanted it to access.
I got the email address (something like xxxxxx@developer.gserviceaccount.com) for the service account by looking under the “API Access” tab in the Google APIs console.
Then, I followed Google’s instructions for adding an email address to an Analytics profile. Now everything’s working as expected.
Good luck!