Google MU is not working correctly

I know that I chose Domain Mapping and my question is related to Analytics but I had to remove it while testing, and trying to hard code the solution.

So when I installed it through the site this is what would happen.

1. All the sites would track...
2. Referrals turned into another visitor. Skewing the numbers.
3. Not sure how to set this up correctly.

Your help will be greatly appreciated.