The bitcoin protocol is working fine gentleman. Just some bug in wallet software which causes this: https://en.bitcoin.it/wiki/Transaction_Malleability. There is already a technical implementation for this and it is implemented now. That's why BTC-E and Bitstamp are updating their wallets.

edit: Gox did fuck up more than other exchanges because their coding was old, therefore the chances of transaction malleability happening at gox was higher.