By “layers” in an emitter, I assume you mean particle types. Just to be clear:
Layer
Emitter
particle type
particle type
Super Emitter
Free emitter type
particle type
particle type
Free emitter type
I know what you’re saying, and that sounds like a bug when loading a project — the “enabled/disabled” state should be preserved. The toggling of particle types when the parent emitter is toggled — that’s how it was designed. I do see the need for preserving them though — don’t know how to best implement this.
Alan.
wondertouch