I found the reason for mismatch and the wrong results in taxes in version 2.
It’s cause by the way “core/fn_cart.php” calculate the taxes and how “js/exceptions.js” calculate them.
It’s happend when you have a product with options and more then 1 tax.
Fn_cart.php calculate the product + first tax and the result + second tax,
exceptions.js calculate the product plus the result of two taxes separatly who that give a few cents of difference in the the second way.
It’s only happend in the cart_item.tpl, all the other taxes calculation are ok.