Extruder clicking issue with MKS Board v1.5 So I know there have been several clicking Extruder threads but have not found any solutions to the one I am having.

Background:
I have a custom Prusa like 3d printer fitted with an MKS board (v1.5) and an MK3 Extruder.

The issue:
While i can extrude fine when ordering some extrusion, as soon as i start to print an object the extruder just starts "clicking".

What I have tried so far:


Changing motors: I have tried using a new motor which I know it
works and the problem persists. 
I have adjusted the stepper driver voltages, and the problem
persists.
I have changed the PSU and the problem persists.
Changing the whole board: I have changed the whole board with a
brand new one and the problem persists.


I am out of options here. So now the only logical explanation is that the both boards (the old and new) have exactly the same problem, i.e. the extruder stepper driver is bad in some way. Yet again, it works fine when simply extruding...

Any help would be much appreciated. 
Thanks.
There is one reason why extruders "click": the material can't be melted and advanced fast enough.

There are two likely reasons why your extruder works when used manually, but not during a print:

1. The temperature is not hot enough for the speed (volume per second) demanded by the print. 

Have you verified that you're using the proper temperature, and that the head is reaching the proper temperature?

2. There is too much resistance on the delivery. 

Have you verified that the Z positioning is not too close, causing back pressure and interfering with the deposition?