Neil,

If I am reading this right, you dont have the ref from the ECU to the CTS. That being the case you shold verify that the ref is missing and not being pulled down, either by a short or another sensor. You could snip the wire close to the ecu to see the ECU is putting the ref out or not. If not and as long as the ECU has its correct supplies and grounds (tested under load) then I think you have diagnosed a faulty ECU.

hth