Peter Shor showed that two of the most important NP-intermediate problems, factoring and the discrete log problem, are in BQP. In contrast, the best known quantum algorithm for SAT (Grover's search) only yields a quadratic improvement over the classical algorithm, hinting that NP-complete problems are still intractable on quantum computers. As Arora and Barak point out, there's also a problem in BQP that is not known to be in NP, leading to the conjecture that the two classes are incomparable.
Is there any knowledge/conjecture as to why these NP-intermediate problems are in BQP, but why SAT (as far as we know) isn't? Do other NP-intermediate problems follow this trend? In particular, is graph isomorphism in BQP? (this one doesn't google well).