The placement of the targetGeom channels in the channel stack is important, they should go above the any of the joint parameter, Offset, or transform channels for correct operation. In my tests in P6 the script has so far always created the channels in the correct location in the channel stack. As to the order of the targetGeom channels amongst themselves, I don't know how that is determined, but it is usually not relevant. If these are joint correction poses, I guess it is possible that the morphs are meant to go in none standard places in the channel stack. If that's the case, then I'm afraid you are sunk, because the script is designed to avoid that.