Interesting post this. It was the same symptoms that my site was displaying, the javascript non-working shopping_cart.php.
I did exactly as stated here, and yes, it did work beautifully. BUT, after that, when I went to checkout, it stayed on checkout_shipping.php, and would just loop, not going to checkout_payment.
ANy ideas on this one? I can't see why this should affect the checkout process, but when I put the standard cart box back, the system worked fine again.