I just wanted to add that I'm having issues as well. I have the latest revision of Melodyne 4 editor. A couple weeks ago I used Melodyne to create a tempo map in a project using last month's Sonar release. I haven't touched the project till last night after updating to this month's Sonar release. The project was completely ruined.
Tracks were merged onto previously deleted tracks. Random clips were merged together. After an hour of trying to clean it all up and make sense of it all I just deleted the project. Luckily I created a backup before using Melodyne. I won't be using Melodyne with Sonar anytime soon. I've had relatively few issues with other projects not using Melodyne. What a waste of $400.