Mark,
check the following parameters for each rank:
Samples_AssumeTunedToConcertPitchAndEqualTemp = N
Samples_RankBasePitch64ftHarmNumIfAssumedTunedToConcertPitch = null
Pitch_RankBaseOutputPitch64ftHarmonicNum = 8 (for 8' pitch rank)
Pitch_MaxRandomTuningErrorHz = 0 (start with 0, adjust later if desired)
Pitch_PipeMIDINoteNum036_TuningAdjustPercentSemitones = 0
Pitch_PipeMIDINoteNum096_TuningAdjustPercentSemitones = 0
Load the organ in equal temperament and see if that changes anything