You mean when you cloned the tracks? Do you mean the ProChannel strip (in the Console View)?
If so did you have the Prochannel open on the track you cloned in the Console View?
That might be it. Close the Prochannel pop out of the track you intend to clone and maybe it won't happen.
Unchecking the "Properties" box in the clone track dialog may keep it from happening as well (not sure exactly what that does but I think it might affect such things).
This is all just guesses though as a) I've never experienced this and b) have not yet installed JP. I also don't use the CV Prochannel popouts (but have been meaning to).
Cheers and welcome to the forum.
edit: oops... I glossed over that part. Still maybe check it out. Not at my DAW right now.