Noel,
I looked in the Separations folder but it was completely empty. I played the project with Melodyne in that region while hovering over the disk icon in the control bar, but no spikes.
I copied the project to another hard drive with more space and ran it from there, and the glitch disappeared. So then I went back to that project on the full hard drive and it started working correctly there too.
I tried some other random project and Melodyne worked as expected. I am now unable to reproduce the problem consistently. I will keep an eye on this and if I can come up with something repeatable, I will let you know.
In the meantime, I can only imagine how you are going through possibilities and scenarios in your head even during your time off. It just shows the pride and dedication you have to this excellent DAW and company. I just want to recognize your efforts and say thank you for your care and hard work. I and many others really appreciate what you do. I could not do what I do without SONAR, and SONAR is what it is today thanks to you and the whole crew at Cakewalk headquarters. I am so thankful for Boston (because of Cakewalk) that I even stopped hating the Patriots for knocking the Chargers out of the playoffs a few years ago. I will even watch and cheer for them during the AFC Championship game against the Colts.