+1 for vector76's hypothesis from me as well.
This seems a lot more likely than my double block mining hypothesis. This would also be harder to protect against.
Anyone have ideas about how to stop this sort of attack?
When the block chain forks, the "true" chain is ambiguous by design. The algorithm only promises that it will resolve eventually.
There might be ways of reducing the likelihood of this attack, but it is inherent in the system. You stop it by waiting for several confirmations.