Note also that a $100 Trimble Thunderbolt available on eBay can get you reliable timing results to within about +/- 20 nanoseconds, given a good GPS antenna.
Compensating for special relativity in the timing calculations was a job that had to be done, and done perfectly, long before the first GPS satellite was launched.
My guess is that the bug will indeed turn out to be a relativity issue, but a consequence of GR rather than SR, arising from the fact that the detector cavern is under 1400 meters of rock.
I'm afraid that unless the Monolith is somewhere under Gran Sasso, those effects are completely negligible. The time scales of the experiment are very short indeed (1e-9 seconds), but the influence of General Relativity is even smaller (1e-15 seconds).
The point to remember that there are so many possible factors that could mess up their results, that the error estimates that were published by the OPERA team were way too low.
Compensating for special relativity in the timing calculations was a job that had to be done, and done perfectly, long before the first GPS satellite was launched.
My guess is that the bug will indeed turn out to be a relativity issue, but a consequence of GR rather than SR, arising from the fact that the detector cavern is under 1400 meters of rock.