You forget one crucial thing in the experiment. A neutrino reacts with almost nothing. A photon on the other hand, react with almost any damn thing you place around its path - metal? Yes. Mirror? Yes. Wood? Yes. Air? Yes!

I very much doubt they completely vacuumed the path of the neutrino to the same degree as it is in outer space. It is possible that neutrinos travel at the same speed as light in vacuum, but travel much faster when there's other material present in the way.