Is it possible that the missing funds were the remainder of a previous transaction and were being held on a "change address" so that when you changed wallet copies the new wallet (presumably restored from a private key) no longer contained the address that was being used for the change of a prior transaction?  That would look like your funds just went missing if you didn't understand how your coins were being managed inside your wallet.  Maybe look at the history of transactions and see if you can identify transactions that sent leftover funds to a change address or be more clear about how you changed your wallet and if it was restored from a private key or any other useful details.