In your cart object definition do you have the ID field set up as 'text'? By default it is an integer and that might be causing issues.
Once you update it to text you would have to re-apply the add to cart server behavior and then that could fix the problem. Do you display the ID on the cart page? I'd do that to make sure it is set correctly first then we can look into why it isn't passed correctly once we are sure it is set correctly in the cart.