Is there concrete evidence in the block chain? Are there indeed altered transactions in the pool? Is Mt. Gox blowing smoke?
In my opinion, the answers are no, possibly, and yes.
The issue is that I create and broadcast a transaction with TxId "X". Someone can tweak it to an equivalent (same send and receive addresses) transaction with TxId "Y". Assuming everything else about the transactions are valid, either one (but not both) might get pulled into the blockchain. I say there's no concrete evidence in the blockchain because the TxId only has an unambiguous meaning once it's incorporated into a block. At any given time, it's possible that both "X" and "Y" flavors of a transaction could be floating around in different unmined tx pools, but any given miner should only accept one. I think Mt. Gox is blowing smoke because everyone else seems to be able to deal with this issue satisfactorily, and the issue by itself doesn't explain all the problems folks are seeing at Gox.
Do you work for Gox?
Have you seen their code?
If not, then you are blowing smoke, and contributing a smokescreen to a market-manipulation coin-robbery of epic proportions.
If any exchange wants an independent review of their code, and a productive environment in which to fix any problems found, I will do it at no cost for code that will be disclosed to the public. If you have proprietary exchange code, my retainer for an NDA starts at $5000.
We have a bunch of guys with NDAs and 'secret proprietary code' all running around issuing press releases about how the other guy sucks, while the handlers that pay their bills are scooping up all the bitcoins they can before the heroic developers, who have been working on this day and night, issue a magical fix and the price of bitcoin doubles.
If broadcasting transactions to the entire network was a good idea for bitcoin, it's probably a good idea to broadcast the code that runs exchanges too. Unless you like handing your money over to the banksters, in which case I guess I can take your money too.