Quad rebuild- One Motor spins up to high speed preventing takeoff

Hi all,
I have a problem with motors spinning up unevenly and I would greatly appreciate any help, so thanks to anyone who can get through this. Its a bit long.

I am completely rebuilding a Seeker with new everything except the motors.
This is what I have: (a brain dump of everything I can think of)
4x Wltoys motors
Kakute 32f7 V1.5 flight controller running betaflight (installed pointing the 
right way)
Racerstar rev35 35a 4x ESC  using Dshot 150. (Motors are correctly mapped)
Beitan gps and mag
3s battery in good condition.
Jumper T-lite remote
accelerometer calibrated ok.

When the Betaflight/laptop is connected to the FC all is well. The motors spin up 
smoothly in sync and everything works ok.
I put the props on (checked all spinning the right way- air is blowing down)
When I connect the Jumper Tx and raise the throttle, motor 3 spins up to high revs and the others stay at idle.

While it is sitting flat on the ground outside (GPS sats visible), when I move the sticks for roll, pitch and yaw the appropriate motor pairs speed up or down, but when I raise the throttle just motor 3 speeds up a lot- so the quad tries to tip over. 

If I hold the quad down and move the throttle up the other motors increase but not synced enough to let it fly.
I haven't changed the PIDs and as I have read, the Dshot protocol doesn't need calibration. All the receiver mapping looks right in betaflight.
I swapped the motor wires for motor 3 and motor 1 and the fault moved so its not a motor problem.

In addition, I have swapped the FC as I bought 2 new identical ones with the intention of building a mini. (if I ever get this one going!)
The ESC is new and I haven't flashed it or changed the setup.
I am new to quads and I'm an electronic engineer so hopefully I havent made beginner mistakes, but feel free to tell me if you have any ideas
Thanks for reading.

Please have a look at this article as it should help you narrow down the source of the fault.