Hello Don,
I assume you are using the example from the 2nd St. Anne's CODM file for the Great Nazard. The setting of <Samples_MIDINoteNumIncrementFromPipesToSamples>5</Samples_MIDINoteNumIncrementFromPipesToSamples> is actually a small error in that CODM file as it should be set to 7 which eqauls a fifth. However this isn't the field which determines what pitch the samples get played back at, for that you want to modify the field called <Pitch_RankBaseOutputPitch64ftHarmonicNum>24</Pitch_RankBaseOutputPitch64ftHarmonicNum>.
No matter what the original pitch of a sample, if this is set to 24 it will play it as a 2 2/3 rank based on either the pitch embedded within the sample, or if they are specified as tuned to perfect concert pitch. Since the <Samples_MIDINoteNumIncrementFromPipesToSamples> was set to 5 Hauptwerk would be repitching them up 2 semitones to account for the missing 2 steps. So, set this to 7, thern set the rank base pitch to 24 and it should be correct.
We'll look at correcting the CODM ODF for the next version of Hauptwerk, sorry for those errors.