I too was having the error where the tracking code was not being printed, as well as the closing body and html tags.

The problem, it turns out, was that I copied google_analytics.php to the wrong directory. I had it incorrectly in /includes/templates/custom/common/google_analytics/google_analytics.php... when it should have been /includes/templates/custom/google_analytics/google_analytics.php

Dumb mistake I know. I read through the last 10 pages of this thread and noticed it's a common problem... so just a heads up.