I'm seeing similar results, and unfortunately, I have neither a good explanation, nor a solution at the moment.
I've experimented a little bit with enabling additional compiler optimizations for the Python 3 branch. That does result in a ~20% speedup (from 1:10 to 0:59), but it's still significantly slower than running it with Python 2 (0:35). Interestingly, changing the integer literals to explicit longs in Python 2 brings it down to 0:50, so very close to Python 3, where all integers are longs, but that doesn't really explain why there isn't much of a difference on the desktop...