I'm having the same problem for some time now and started a thread back in may about it.
https://forum.cockos.com/showthread.php?t=221137
This post to say that, I've always managed to find a working version (with all Melodyne data correct and not complaining) in the last backups (I have auto backup set to 2 minutes).
Which is why it seems unlikely that this problem is config related, as some RPP projects work and some don't including backups.
However, I did try to delete all my .ini files this morning, to no avail, I got the same error from Melodyne.