AFAIK both implement the same basic algorithm. My guess is that nauty quickly realizes that it has a huge problem and starts constructing graph invariants in an attempt to answer it to the negative. If you were to compare two graphs that are actually isomorphic I'm pretty sure that you wouldn't find such a big difference. For practical applications it is of course important to have this trick using easily-accessible graph invariants, but its probably not that hard to implement..
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