Read the whole thread and the corresponding articles linked to in it. It doesn't actually really even affect Bitcoin.  It affects Mt. Gox and how they determine if you received the BTC they sent you - Mt. Gox looks for a Transaction ID on the blockchain that they stored locally at the time a user requests a withdrawl.  Transaction ID's can be changed or mutated, and until they are committed to the blockchain, are not cemented in stone, and may change.  If you look at your inputs, outputs, and transaction times, that is proof enough to determine if a transaction went through or not.

Mt. Gox apparently did not investigate claims of BTC not being received very well, and manually sent second payments because they did not find their locally stored Transaction ID's on the blockchain because they were transformed before being committed to the blockchain.