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In the updated wallet, we have implementing Checkpoints – Simply put, it prevents attackers from replacing the existing chain with a different chain. So protects against transaction reversal. Checkpoints are built into the Bitcoin code and all its alts, they are defined as a block height and its hash, the Bitcoin software will only connect to chains with those checkpoints in.
Automatic Checkpointing is real-time checkpointing, rather than define them in the code they are broadcast from a node on the network. In the source code there will be a public key, only a node with a corresponding private key can send out checkpoints, that node will also need to configure a depth for the checkpoints, that is how many blocks there needs to be after a block before it is checkpointed, so a depth of 5 means that a block will be checkpointed when there are 4 confirmations for it making it 5 blocks deep from the top of the chain.
Read more in Bitcointalk – The update 220.127.116.11