Just to clarify we are listening only to that Organ RT which has no notation right? I have the chords playing on Utility #1, but that is just my default. So I will mute those which by the way does have notation and is spot on.

That specific organ RT sounds like a Hammond B3 with draw bars which intentionally add upper harmonies such as the 9th and 13th - it is just the nature of that beast. I have recently been playing a B3 and it is a marvel at what extra sounds are added based on setup of the draw bars.

If I am correct, than if you substitute a Piano RT for the Organ you should see everything settle down in your chord notes. I know you want the Organ, but you may just have to settle. Or perhaps you could try new Toontrack B3, where you can edit the beejeebiz out of the instrument and eliminate the draw bars. Just a thought.

... btw, I just tried to add the EZk2 Session Organ as a plugin on the Chords Track to hear it play over these chords, but alas... BIAB is not compatible with VST3! mad

Lets see what others have to say...

BIAB – 2025, Reaper (current), i7-12700F Processor, 32GB DDR4-3200MHz RAM, 1TB WD Black NVMe SSD, 2TB WDC Blue SSD, 1TB WD Blue, 2 TB SK NVMe, 6 TB External, Motu Audio Express 6x6