I would like to apologize for late answer.
@majolo - after you bought Eco, did you take apart the pen and put fresh portion of grease on the piston (before fist use)?
I might have a theory that the grease put on piston during assembly of pen in factory is different than that used in case of 540/580 and the one provided with pens. And the interaction of grease used in assembly with ink causes the problem.
Some silicon greases are made by mixing significant amount of fumed silica or similar compounds as viscosity modifier and silicon oil - this is one of simple ways to make good quality silicon grease of moderate viscosity and good lubricating properties. But there might be a problem if silicon oil would be extracted from the grease - than what would be left behind is fumed silica - silicon oxide. Silicone oxide is pretty abrasive and is hard enough that it could scratch the inside of the barrel. This is something I encounter from time to time in my laboratory work and can be quite a problem in case of glass-glass joints. I have also saw that rod of full glass mechanical stirrer that was placed in PTFE fitting became "cloudy" after some time, and this was most probably caused by highly viscous silicon grease that was put in the fitting to provide better seal.
Why I do not think this is any interaction between ink and plastic? Well I have an Eco in front of me that I filled with IG Green #3 in October, I put new portion of ink in February. I just moved the piston and it is perfectly clean and transparent where the piston moved. Also on @majolo picture the only place which is cloudy is where piston was moving - the section and bottom of barrel are perfectly clean.
Why in my Eco there is no problem? Well I have seen/heard about some issues that if piston in TWSBI was not greased than after some time it had tendency to got stuck - so the first thing I am doing after buying one of TWSBI pens is taking the mechanism apart and putting grease on the mechanism and on piston.
What could be the solution in this case?
Washing the pen throughly in ultrasonic bath with detergents. If that doesn't help than putting a bit of silicon oil to the barrel and start scrubbing it gently with something that has a rubber tip or some soft wood (like from long matches), this way you could gently remove any residue from the inside of pen and "polish" it a bit.
What can be done to confirm this theory? I think I will buy two more new pens I will use the same ink in one pen that was just taken from the box and one that was taken apart and greased before first use.
I would like to apologize for any problems that could be caused by inks made by me and I will try to help resolve all the problems as fast as possible.
About other theories:
TWSBI pens are made from polycarbonate there is nothing in the ink that could react with it or similar plastics.
It is impossible that iron oxide would be formed in the ink. No air, IG component, plastic could lead to that. Also the scratches than would be red-brown.
Other iron compounds that are present in the ink or could be present in it are easily soluble in water.
Insoluble complexes that are formed on paper would be deeply colored - and also they are way to soft to scratch plastic.