Light can move more slowly while not in a vacuum, maybe this light was held up by something. That said, I don't understand the paper well enough to tell if they are directly racing the neutrinos against some actual light, or if they're just comparing it to an earlier mesurement.
I don't know whether this guy knows what he's talking about, but it sounds plausible:
Steven Sudit:
...The speed of light in a typical vacuum false short of the speed in a perfect vacuum. Light is slowed by interaction with particles, even the virtual particles found in a vacuum. This is why it's slightly faster when passing between plates exhibiting the Casimir effect, since that's based on suppression of virtual particle creation. (http://en.wikipedia.org/wiki/Faster-than-light#Faster_light_.28Casimir_vacuum_and_quantum_tunnelling.29) So one plausible expla
http://www.nature.com/news/2011/110922/full/news.2011.554.html
http://arxiv.org/abs/1109.4897v1
http://usersguidetotheuniverse.com/?p=2169
http://news.ycombinator.com/item?id=3027056
Perhaps the end of the era of the light cone and beginning of the era of the neutrino cone? I'd be curious to see your probability estimates for whether this theory pans out. Or other crackpot hypotheses to explain the results.