Grasping at straws no doubt, but have you checked if you don't have any blocks in your drawing that could contain those offending layers?
Another suggestion.... what with it disappearing and re-appearing..... did you check your drafting standard?
I think this finally got solved, thanks to this Discussion: How to set the default layer to -Per Standard- . I'm marking this Discussion as "Assumed Answered". I can't in good conscience mark my own answer as correct when I didn't figure it out on my own.