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No, they weren't counting down at all because they weren't supposed to be counting down. The confirmations listed by Slush is basically the number of blocks built on top of the block in question. IE, for block 331733 (
https://blockchain.info/block/00000000000000000d85f2d73089f2420d3f71d4a614139ace6bab56888adbc1?site=slush), Slush will consider that confirmed and pay out for it after the network all together finds another 100 blocks. After 331733, no blocks were found for 40 minutes, and that's why it stayed as 100 confirmations required, and none of the other blocks were counting down either.
As a point, until a block has at least one built on top of it there's always the chance it can get orphaned, but it would actually be very unlikely for even the last block to be orphaned after a couple minutes or so. You get orphan races when two blocks are found within usually a couple seconds of each other, but after a minute everyone who's not running broken software would have been mining on our block, and not the preceeding one.
Just a couple of points.
In the current bitcoin-qt it's 101 blocks
When I added that to the ckdb code I was surprised to see it is actually 101 not 100 (as I also thought it was 100)
But that's also due to the confusion that when a block is found it is considered 1 confirm, not 0 confirms.
Although an orphan race is usually obvious, if someone finds a block after most people on the network know about another block, they can keep mining off their own block and win if they are very lucky.
Of course they would have to not send out their late block, thus the network wouldn't know about it at all.
But if they are lucky enough to build on their own block before anyone find a block to build on the network block, and they send out both, they will actually win the previous orphan race and their 2 blocks will become the network blocks.
So yes, even I look at the 'known' blocks when my pool finds a block and am usually pretty sure after a few minutes, but it's still not certain.
Of course, if you are looking at blockchain and not in your bitcoind debug.log the losing block may be on the network and you just can't see it in blockchain.
That's rare but it can happen.
The normal thing that happens on an orphan race is that part of the network will be mining on one and another part of the network on the other.
It's then purely up to which part of the network finds the next block, that decides the orphan race (though it can in rare circumstances be longer than 1 block to decide it)
So it just depends on who has seen both blocks, to know that the orphan race is even happening - but normally everyone has seen both and chosen the one they saw first, to mine on.