(I *am* a physicist) Actually, the original paper *did* measure time with GPS - more to the point, they use GPS to establish a common frame between the two locations. Look at Figure 5 of the OPERA paper (http://arxiv.org/pdf/1109.4897v1).
Having said that, as other replies have noted, this kind of correction is well-understood, so while it isn't explicitly laid out as far as I can tell, it's unlikely the OPERA group screwed this up. What may well be true, though, is that there may be systemic offsets either in the GPS timing system, the implementation at Gran Sasso (they actually have a big waveguide that they run from the Earth's surface all the way to the GPS reveivers they have by their detector deep underground), or any of the myriad corrections that were needed to determine the time-of-flight baseline (although as far as I can tell they worked very hard to get this measurement right...).
It's also rather suggestive that the author of this paper has no particle physics (or even physics) credentials. So he/she probably doesn't know the OPERA collaboration's processes very well (admittedly, these details should be in the paper, but the tradition of the community is to not do that sort of detail in announcement papers like this...)
Source: http://rss.slashdot.org/~r/Slashdot/slashdotScience/~3/XtHyUufg0MY/ftl-neutrinos-explained-maybe
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