Update:
I've gone down to Mann Motorsports (
http://www.tmannmotorsports.com/page/3394,
cheezey website but they are great guys) today and one of Tonys guys hooked up their new Autologic computer to my car, and it wouldn't clear the codes either.
The dealership I go to and have spoken with want me to buy a new BST (Battery Safety Terminal). The one I have should be perfectly fine though.
