This question is kind of old, but I have been researching because I had the same problem. Turns out GA doens't track visitors with javascript and cookies disabled. This could also account for a part of the non registered visits by GA.
I suggest you check the server logs. You'll probably find the data match there 
More resources here:
http://cse-sea.blogspot.com/2009/09/troubleshooting-discrepancies-between.html
http://productforums.google.com/forum/#!topic/analytics/cotsK2GNh_w
Hope this helps someone else with the same problem.