The only logical explanations to me are thus:
Some technical limitation meant that the miners at the time (there weren't many) weren't searching some nonces as they should. Everybody was using the built in miner then, so it's probably easy to check if there's an old enough SVN around.
The miners at the time intentionally binned certain nonces to avoid hoarding all the coins, keeping the difficulty low. The difficulty was barely 1 at that point, so I don't think this is an unreasonable assumption.