If you notice issues where on your store some products fail to add to the cart. Usually when this happens it means amazon has throttled your API keys, this only happens for a few seconds and then API will retry to update the products.
The reason sometimes adding to the cart fails is because amazon throttled your API keys and the product failed to update so it couldn't be added into the amazon shopping cart. This is a limit by the Amazon API and we are always looking ways to improve it.
What I recommend customers with big stores is to enable "Buy At Amazon" Buttons only. This is what I personally do for all my stores, I have disabled the shopping cart and only use the "Buy Amazon" buttons.
Please see links to articles below for more information on Amazon API throttling, what products can't be used with amazon shopping cart and a video that explains the shopping cart cookie and the 24 hour cookie.