Was Einstein Wrong?

The time of flight measurement does not appear to be between that of two discrete events, but rather between two distributions of events. As best I can make out, there is an underlying assumption that there is a linear correlation along the time durations between the two distributions. I think that is also what the author of this article is getting at in his critique:

http://www.guardian.co.uk/science/life-and-physics/2011/sep/24/1?newsfeed=true
 
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