This is how the controller should be working, Your turn the vehicle on
you see a red power light and get 3 flashes of the 3rd LED
You drive the vehicle and you hit your starting pressure/voltage point the green light will come on then get brighter as the voltage increases.
The 3rd LED will only come on at 95% of the full set point/ pressure/voltage it will flicker if it is just about at that point, after that it will remain solid.
Is this what the controller is doing? Now if you have a MAP sensor that reads in microvoltage for the lower ranges which many 3.3 bar map sensors do then the controller will not work right until it sees the right voltage.
Did you measure the voltage that the green wire is getting under throttle yet?
The controller is based on the GM 3 bar scale for voltage and cannot read microvoltage so if your map sensor has this it is just like no voltage present for the controller so it will hunt for a signal.
To find out for sure it is your map sensor you can base your injection off the MAF by connecting the green wire to the 5 volt output on the MAF which is D
