Hi Kevin,
I don't think it is a bug. Once you edit an instance you basically take responsibility for it's position, size and orientation. For example if you've changed the scale of an edited instance then it wouldn't be right for the populator to change it because its scale params have changed. Even if you haven't changed the scale explicitly, TG can't know if you were happy with the edited instance at its current size or not.
Regards,
Jo