The neutrino generation is somewhat indirect. Protons are accelerated into graphite, and then the resulting particles are accelerated further in the correct direction so that they decay into muons and muon neutrinos. The muons are quickly lost (muons don't like to interact with much but a few kilometers of solid rock will block most of them). The detector itself is setup to detect specifically the neutrinos which have oscillated into tau neutrinos.
The detector itself is a series of lead plates with interwoven layers of light-sensitive material which has then scintillator counters to detect events in the light sensitive stuff. I don't fully understand the details for the detector. (In particular I don't know how they are differentiating tau neutrinos hitting the lead plates from muon neutrinos or electron neutrinos) but I naively presume that there's some set of characteristic reactions which occur for the tau neutrinos and not the other two. Since this discrepancy is for neutrinos in general, and they seem to be picking up data for all the neutrinos (I think?) that should't be too much of an issue.
I've heard so far only a single hypothesis of new physics without faster than light travel involving suppression of virtual particles and I don't have anywhere near the expertise to guess if that sort of thing is at all plausible.
The detector itself is a series of lead plates with interwoven layers of light-sensitive material which has then scintillator counters to detect events in the light sensitive stuff. I don't fully understand the details for the detector. (In particular I don't know how they are differentiating tau neutrinos hitting the lead plates from muon neutrinos or electron neutrinos) but I naively presume that there's some set of characteristic reactions which occur for the tau neutrinos and not the other two.
There is a conserved quantity* for elementary particles ...
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.