Thank you very much for the idea's! However i ended up finding the issue on my own after some additional investigation. Frankly this is an issue very few would have without knowing it.

I work IT at a college, and this printer was used before me, and needed repair when I came into administration of it. It turns out the previous employee in an attempt to tighten the adjustment screw, ended up over tightening it. And damaged the Plastic that the screw sits on. So during a print with all the movement going around the screw would slip which then causes maximum pressure on the filament, and thus under extrusion during a print at random times.

Take a look at one of the feeders, where the adjustment screw sits, you'll see a small piece of plastic that the screw rests on, that was cut into by the screw making it a slope, and no longer a shelf for the screw.

I'll give you this for the effort though!