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I'm pretty sure PECPrep is the only (native) EQMOD solution that will automatically sync the PEC with your steppers Brendan. If you use any other program you have to click the TimeStamp button on the EQMOD driver at the same time you stop recording data. This presumeably writes data somewhere to show where your steppers were at that moment so that when you next load up your PEC it will start at the right point. I've done this when I recorded my PE data via Maxim and it worked ok.
Perhaps you just happened to be roughly half a cycle out of step when you fired it up?
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