GPS? The emitter and detector are underground, so I wonder how they got an accurate GPS measurement. If they just have a GPS receiver aboveground, how do they know that that accurately corresponds to the location of the OPERA equipment? Are there survey markers on the land covering CERN?
Anyway, to double-check their results, they just re-ran the experiment a couple of thousand times. They didn't try shooting anything else with a known velocity to see if that gave anomalous results. They don't mention anywhere recalculating the distance between the emitter and detector. All they did was run the experiment again and again. If they made an error early on, of course they would continue to get anomalous results.