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
60 nanoseconds ~= 60*30cm ~= 18 meters.
I kind of doubt that lousy connection would make the timing signal arrive 18 meters late. That requires the signal being re-sent and arriving only on second, third, and so on attempt.
Maybe that could happen between consumer grade routers which have such complex algorithms as to have for all intent and purposes non-deterministic timing, but if they were using that to send time in this lab we don't need to find lousy connections to discard the results. Scratch that, i don't think this can happen with consumer grade router, that it would resend same packet at brighter and brighter light level until it gets through, or the like (then forget about the brightness and do it every time). The computers re-send stuff when it is TCP protocol, and when it is UDP they don't, and who in their mind would use TCP for time anyway.
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.