The original computation did not take into account the initial phase shift. A corrected computation, included as section II in the revised version of gr-qc/0407039, still gives a term proportional to the derivative of the signal, qualitatively confirming the original result.
Cite
@article{arxiv.gr-qc/0409099,
title = {The gravitational phase shift in a matter-wave interferometer (MIGO)},
author = {Stefano Foffa and Michele Papucci and Riccardo Sturani},
journal= {arXiv preprint arXiv:gr-qc/0409099},
year = {2007}
}