Are you sure they are two different blockchains? Or maybe you just haven't downloaded enough blocks..
Definitely 2 completely different chains. I had 10 confirmed blocks + 2 immature blocks beforehand. After using the checkpoints and redownloading the blockchain I had 0.
At the time I write this getinfo reports the block number to be 8247.
I think I'm with you (8479 now) but we need someone that can set up an ABE or block explorer to see if we have 1600 (or whatever) blocks mined by the same person at the start of the chain now.
Did you pull milkshake's latest git and all when you set the checkpoints? If you did I'm staying on this chain and going to bed.
Sorry I don't have the skills for it or I would be checking this myself, too.
edit: I guess it would just be enough to see the phrase in the first block, right?