pls. check note selection too
seems ok with closed voicing, so it's a custom voicing related issue (I've played with the Chord Voicing Editor (which is supercool) before I've began to use the phraser)
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and yepp,
I am sorry for the misleading note labels (Root, 3rd, 5th) which actually mean 'chord lowest note', 'chord second note', 'chord third note' but can be entirely different notes when voicing is used. E.g. when you omit the root note, the lowest note will still be displayed as 'Root' (Internally the modified chord will have the 3rd as the lowest note)
should use some pre-postfix to able to distinguish the voice index and position index (dunno for ex. p3rd or i5th etc. )