Hello,
In the Rank table in your CODM ODF, check the following entries (see also the CODM user guide for an explanation of each setting):
Samples_MIDINoteNumIncBetweenSamples = 1
Samples_AssumeTunedToConcertPitchAndEqualTemp
You either need to have the exact correct pitch stored in the samples, or else Samples_AssumeTunedToConcertPitchAndEqualTemp needs to be set to Y. If Samples_AssumeTunedToConcertPitchAndEqualTemp is set to N then Hauptwerk will attempt to read the pitch from the sample files, so if they have an incorrect pitch value stored in them (in the SMPL WAV chunk) they would play at the wrong pitch.
For Hauptwerk's temperaments to be able to work Hauptwerk needs to know the exact pitch of each sample, which can either be done by tuning the samples perfectly to A-440/equal and setting Rank.Samples_AssumeTunedToConcertPitchAndEqualTemp=Y or by storing the exact pitch in the WAV SMPL chunk and setting Samples_AssumeTunedToConcertPitchAndEqualTemp=N.
If you haven't detected the pitches or retuned the samples then you can still set Samples_AssumeTunedToConcertPitchAndEqualTemp=Y, which should allow them to sound at the original pitch (as Hauptwerk v1 did), when equal temperament is selected in Hauptwerk, but other temperaments will not then work properly.