The tech explanation doesn't add up. Is he saying they were the victim of double spend attacks?
That's the only reason 1 vs 1000 confirmations should matter.
It would be so hard to pull off a double spend in this manner that this still smacks of BS.
Not only that - if they were the victim of double-spend attacks, they should be able to provide copies the duplicate transactions spending the same input, and probably even the two blocks with different versions of the same transaction. (The official Bitcoin client stores orphaned blocks it saw that used to be part of the main chain pretty much forever.)
A double-spend with only 1 confirmation might actually be doable in this case, though, because an attacker can just keep trying repeatedly until they succeed at little or no cost to them, and because synchronization of blocks between the big mining pools isn't very good even at the best of times. Tycho's refusal to give the IP address of his Bitcoin node for Deepbit to any of the other pool operators is actually quite damaging from what I've heard.