Chords playing different notes notes that are incorrect

Do you mean that Harmony Navigator ist starting the progression with an inversion? Doesn't happen for me in HN2 Advanced (newest version).

And by the way: An inversion is not a totally different chord.

It probably uses an inversion, because the playing ranges of the instrument require this. HN2 attempts to adjust the voicings of all chords around the typical pitch of the instrument where possible.

The inversion also depends on the history of recently played chords (voice leading).

Try adjusting the typical pitch of your instrument in global preferences (if its a global instrument), or in the devie description that includes the sound.

The notepad does not currently retain the chord inversion. It uses automatic voice leading by default. Use the Progression Editor instead to control inversions manually.