This may seem far afield, but isn't this what Melodyne does if you choose 'Algorithm/Percussive' for processing the audio - all pitches get knocked down to a single level?
(Sort of like what Logic's vocal transformer does when you select 'robotize').
I'm wondering if there's a setting (or a bug🤔) where flex pitch is doing something similar to what Melodyne does in the above case?
Maybe Flex pitch has a percussive option that's somehow set?
Perhaps someone here more versed in flex pitch options knows of some similarity?
Also, what happens if you select all the tones and use the 'reset to original pitch' option under flex pitch?
But I haven't seen this (running flex pitch on Logic 10.7.6) and I use flex pitch all the time.
When you say it's inconsistent and only on new audio material, what happens if you copied one of those new project audio regions (that's exhibiting this) onto an audio track of an old project? What happens then?
Or, by inconsistent, you mean you might flex some audio and it works then record another region on the same track and it flattens it?