I checked if the trigger signal reaches the Duet by extending the pin via M280 P3 S10 , then putting the BLTouch in test mode with M280 P3 S60. The Machine Status panel of DWC shows a Z-Probe value of 0 when the pin is extended. I Lightly touched the pin on the BLTouch to retract it, 
DWC turned red and show a Z-Probe value of 1000. 

Without changing your config and your wiring, I checked the status of E0 in the Machine Properties tab of the Settings, and did the same test with  M280 P3 S60  to see the BLTouch signal in the endstop column.

both tested worked showed probe is doing it's part and functioning as intended. What is not, is the firmware/config.g/homing file setup. Something written there is preventing the register of the height @ triggered location and the S1 command to stop is still being ignored.