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When you're looking at 200+ ranking factor, there's a lot we can't account for even across all of our metrics. A few possibilities: (1) The #2 site's links are being devalued, for some reason, due to quality issues. (2) There are geo-targeting signals out of whack or focused outside of the US market. If the site is ranking #1 on Google.co.uk and has a clear UK connection, that could lower it's value on Google.com slightly. It's not the kiss of death, but it can make a difference. (3) The #1 (currently on Google.com) site has recent activity that we're not aware of yet (link-building, especially). (4) As Joshua said, #1 could be targeting inbound anchor text better. (5) As Brandon said, #1 may have an advantage on user signals. I don't think that Google currently "sandboxes" new sites in they way they may have once. What I think we're seeing is a grace period where new sites get a chance to rank while Google evaluates their link profile. If, after a couple of months, those links look spammy, the site may drop. In most cases I've seen, though, that's not a #1 vs. #2 sort of thing.