One thing to note about the blocks from genesis to 30,000 or so is that
a) They, for the most part, all appear to have different coinbase transactions.
b) They are also almost completely unspent.

I think the likeliest scenario is that hundreds of people downloaded and ran the client then, got a bunch of blocks that were at the time useless because they were valueless, then deleted their clients.  Recall that in May 2010, bitcoins were only trading for 0.0025 USD each.  It's my personal guess that these coins are just lost to the chain forever.