Thanks for the detailed explanation.

Do you have any idea of how high is the percentage of discarded transations under "normal" conditions? Would it be feasible for some miners to be logging those "incidents"?

Anyway, one thing is that we can't detect those "malleability attacks" afterwards and other very different that mtgox can't reconcile its internal accounting with the blockchain and detect each and all discrepancies.

Please let me know if theres some reason that a process like this would not work:

1- Balances for all accounts with no withdrawals are ok (at least from a "malleability issue" point of view)
2- Balances for all accounts with no failed withdrawal + reissue are also OK
3- Accounts with failed withdrawal transactions lets check like this:
    - For each failed transaction lets search if the transaction went through. Obviously not using the txid, but ammount, input, output. If it did, then flag the account as "abuser" and take note of the "leaked" ammount.

Now you should know exactly how much the malleability "issue" is to blame for the "missing" BTC's and also who were the users behind it, and when/where the leaked money did go to.

Is there any technical reason for this to not be a simple process to run against mtgox records or maybe the only reason they havent made this figure public is because they already know that total sum would just be negligible and that was not the real problem?

P.S.: I am aware that there have been some comments saying that one of the faults of mtgox was that maybe they were doing the reissue using different inputs...

Well, that's what makes difficult/impossible to locate the "dupes" using only the blockchain, but mtgox accounting records should have the missing information, i.e. inputs/output/ammount for each attempted transaction, original or reissued, so that it would be a matter of going through that records rechecking everything against the blockchain.