Thanks for the advice, I'll try it like that then! I'm doing everything else right, so it must be the layers.
I just tried it quickly myself and it does seem like it works fine with the two shapes on different layers. So, uh, I have no idea what's going wrong.I've just checked this out and looks like all the functions work perfect with the paths being placed in different layers, so I doubt it interferes.
Any chance you could upload the SVG you're working on, CtrlAltHistory?