In my previous reply I was mistaken, getting the value to match up in the cart when you update it is not difficult it just requires making sure you use the proper naming convention for the select list so that the items index in the cart is known from the name of this element.
I'm opening a ticket for you on this topic so that you can post some more cart files privately and I will take a further look at what you have in your pages and help try to figure exactly what is going wrong.