Tossed and turned all night with this problem kicking around in my head, could very well be a pinched wire in the main harness from the controls. Have they checked for that? The wires inside the harness aren't much and a sharp bend or even a good sized adjustable wrench dropped on them while installing could produce a break which normally doesn't cause an issue, but when the Gremlins are just right and they move things down there in the engine room, the wire can separate (due to motion, or expansion from any source of heat, or just because they are finicky) it can ignore the signal so the control box is just sitting there wondering what's going on - that wouldn't show up as a fault. Next time you chat with ZF you might see if they would send you a cable and just rig it up right next to the original one installed, wire tie it loosely and see if that helps the situation any.
