EXS 24 Logic Sampler Users Group

If I understand your problem correctly the problem occurs at one specific point in your song. At a certain point in your song some kind of generator of midi data becomes active and starts to add events to your song in different tracks. Is that right? To be sure it's not a bug in Logic 6 you could send a cleaned up version (that you hopefully backed up before the haunting reoccured)  to someone running Logic 7.

I remember the occuring of circular structures when I accidentally hit the wrong key for a key command. Maybe your undo history can tell you more. I had to revert to backup and restart the computer to get rid of it.

Another thing I could think of is an environment thing. Like some output-input-rewire kind of thing though I don't know if that can affect sequences when you're not recording. But you could check your environment for any unwanted objects.

In addition to Hendrik Jan's solution I would first try to save time by playing the tracks solo before getting into saving numerous songs.

Either way, try to play the song on another computer and another Logic version to be sure it's not your computer or software that's bugged.

If you don't know anyone with Logic running you can send the song to me.

Amir