When this happened to me it was on a project I had been messing with AS on. Typically I try to bounce AS edits before save, but those markers only ever showed up in one project (and IIRC was when opening a project, not while working on it). Once I knew how to shut them off, it was no biggie, but having used that method to turn them on was not possible. I have no idea what caused them to enable on that project in the first place.
Is there an alternate method to turn them on that doesn't require drilling into the clip pane menu? Also, this was on X3 that it happened, so may no longer be applicable anyway.