I think I recall reading that they didn't take the orbital motion of the GPS satellites into account, with respect to the difference in inertial reference frame of the GPS clock and the surface clock. They apparently calculated as if the GPS clocks were on the ground, not in orbit.
Ah yes, here we are:
Faster-Than-Light Neutrinos Result of GPS Movement
The motion, once factored in, came to almost exactly the time difference they measured in the neutrino arrival.
In other words, the Tom Tom came out of the dashboard suction cup again.