By putting a recirc. filter in the injector discharge/return line, you change the parameters of the injector return pressure ... increasing pressure in the return line due to the pressure drop of the filter when clean plus accumulating flow resistance as the filter becomes 'loaded'. Such can cause an increasing 'rich' mixture for the injectors, in comparison to a discharge line that operates at essentially atmospheric pressure.
Since your system 'works', let it alone; but, if you later experienced a much high fuel consumption, this may be the cause -- recirc. FILTER becoming plugged with corresponding higher back pressure on the injector discharge line.
Thanks for the answer, but I don't really understand it. The polishing filter is not in the return line. If the polishing filter was completely blocked the engine return would work normally.
The polishing system picks up from the bottom of the tank, to a pump, then the polishing filter. The polishing filter returns diesel to to tank via a T connection on the return line which is between the engine and the fuel tank.
The engine has a separate fuel pickup and filter, but there is only one return to tank which is shared by the engine and polishing system.
This is a common way of plumbing a polishing system.
Perhaps you are only warning about placing the polishing filter actually in the return line so all the engine return fuel has to go through this filter. This is different to engine and fuel polishing system sharing the return line. I can see how the former plumbing would cause a problem, but I have never seen a polishing system designed like this.