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Max has tagged the new version of PulsarSpectrum (now v2r2p2); it includes a simple model for timing noise. He reports that the problem with running the SC1 pulsars on recent versions of PulsarSpectrum seems to have gone away with HEAD1.516 of Science Tools. I don't know why, and have not confirmed this yet. According to the release notes, HEAD1.1516 516 does include a modification to observationSim that has a workaround for how astro::GPS does or doesn't pay attention to start and stop times in the pointing history file. I have not gotten around to asking Jim whether this change could be the explanation for the apparent fix.
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