You say you are creating a smart card application - how exactly the smart card is used? Is there some sort of card reader that is plugged e. g. in the USB port? If yes, is this device recognized in the guest OS when running on ESX? Have you configured properly USB passthrough in order to connect this device inside the guest OS on the ESX server?
To your other question (why the copy is not identical) - it is because these are different products, they have different features and formats, also we are making some changes to the destination during the conversion process in order to make it bootable, etc.