A mundane cause for a surprising result. Consider this unconfirmed for now, however unsurprising it sounds.
According to sources familiar with the experiment, the 60 nanoseconds discrepancy appears to come from a bad connection between a fiber optic cable that connects to the GPS receiver used to correct the timing of the neutrinos' flight and an electronic card in a computer. After tightening the connection and then measuring the time it takes data to travel the length of the fiber, researchers found that the data arrive 60 nanoseconds earlier than assumed. Since this time is subtracted from the overall time of flight, it appears to explain the early arrival of the neutrinos.
New data, however, will be needed to confirm this hypothesis.
Source: Science/AAAS
That's 18 meters for light in a vacuum. GPS receivers and lousy connections are not made out of vacuums. Translating into meters doesn't help us all that much when we are considering hardware faults like this.
18 meters of air, ~12 meters of glass, ~36 meters of going through glass instead of air, and a lot of meters for going through faster glass rather than slower glass when connection is tightened (and don't think of the signal bouncing at an angle and arriving slower, that's not how fibre optics works). If they have a long glass cable, you can be certain that delay has to be actually measured because speed is temperature dependent.
The point of the conversion from nanoseconds to meters is to have some sort of intuitive reference just how much behind the signal must get via lousy connection.