Colin,
Note that the matched filter detection implemented in my model, is far from an optimal detector. If there was any external noise in the system, in addition to the intrinsic noise of the coin, the matched filter would increase the noise power without any corresponding increase in signal power, since it extends far beyond the edges of the coins. An actual matched filter would duplicate the filter used within the coins, to eliminate this problem. I deliberately did not do this in the paper, since it would make the paper and figure harder to understand by the physics community, that has little or no intuitive understanding of such issues.
Another issue is aliasing. Since the image extends only a limited distance beyond the edge of the coin, high frequencies fold-back into the image without being properly attenuated by the filter. These types of issues, along with many others, could easily contribute a 1% error, such as you have observed.
By the way, we ought to move this discussion to a more appropriate web-page. On FQXi, a better choice might be the newly created Quickfire Quantum Qs
I will post a figure and comment there, pertaining to the odd harmonic series of the classical correlation curve as compared to the quantum correlation curve, and a possible connection with detector efficiencies.
Rob McEachern