I've noticed a strange thing where if you have an item which ships FREE for that one product, and add it with other items in your shopping cart, the free shipping for that item will make the whole cart free shipping.
This only seems to occur if the free shipping product is the last added item in the cart. If you added another item, the shipping gets recalculated.
To test:
You can test this on the demo site. The free product I made free ship is "Absolue Eye Precious Cells"
If you have multiple things in the cart, check the shipping cost on checkout.
Now, add the "Absolue Eye Precious Cells" item and check your cart. The whole shipping is now free.
If you go and add another item, the shipping will again be recalculated correctly.
Thanks for testing if you get this.
My guess is the code isn't reapplying and exiting the free shipping section correctly. If you can sort free items to top, that would solve it also.