Hi, I'm afraid I still haven't got any answers. As far as I can see, I have done everything as explained by Googles help page but it is still tracking most transactions as being referred by my shopping cart. I did read the some cookies take months to expire though so this could be an issue?
In terms of your code - the block of code you have pasted in should only be present on the 'thankyou' page (basically the page your site visitors reach after the order has been processed). On ALL of the other pages on your site you should include this code:
var _gaq = _gaq || ;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script'); s.parentNode.insertBefore(ga, s);