When nesting a project some of my audio channels don't show up. If I close VP13 and try again it my or may not work. Sometimes If I change the project name that may work.
About 3 years ago when I had VP12 I had the same problem but never followed up on it. Any help would be appreciated.
Try deleting all of the funny .sfk / .sfl files in projects folders. Check the names of the files with different extensions so they would not duplicate.