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Its possible that the following the could be contributing to what you are experiencing: the guitar is intonation is off and needs to be set up; not getting a hot enough signal to the PF, with this regard try getting the peak LED to light as this would be an indication the PF is receiving a hot enough signal.
We also haven't had any additional reports of any of the effects harmonzing incorrectly or flat, and we don't experience this ourselves. Firstly I would like to suggest that you intitialize the PF to clear out the memory; see manual for this. Afterwards reference the Harmodulator and PitchFlex again and confirm if you experience the same issues.
If you do please follow up with firstname.lastname@example.org so that we can look further into what you are experiencing. Additionally I would like to ask all PitchFactor owners to test these effects with the settings Luca mentions to confirm if any other unit experiences this. If this is an issue we would like to know about this asap and have it resolved for our customers as quickly as possible.