There is definitely something.. I was producing enough oil to run my boilers from 10 mk. I farms with pips filling up a warehouse.. I upgraded them to Mk II which doubles the output and put each step of the process in a factory building... Now I'm running out of output. I even built another 10 farms, and the oil is just not enough. The pips (purple oval shaped icon) should fill the chest, but they are slowly draining away.
I changed over to normal pipes instead of the input/output pipes, and the problem went away a little, but I just changed back - so you will have to wait a little for the pipes to refill to actually see it, currently, the presses are just chewing through the pips while the pipes fill back up with their 2500 each.
(Ignore this save) Savegame: https://www.dropbox.com/s/gz1r9swkru1v7r4/SB3%200082.zip?dl=0
Edit to add: I switched over to barelling most fluids after my last comment, and straight away, my sulfuric waste water overflowed. I might try barrelling here and see what happens. (And in answer to your reply, yes, the sulfur gets used up while the acid is being made, then it refills when the sulfuric waste water is processed. Over time, the amount of sulfur increases dramatically... But it was consistently draining. I was thinking of installing creative mod for the empty barrels and having 2 savegames you could compare, ore with barrels and one with your high-flow pipes).
Edit edited to add that something I did before that save fixed it - possibly replacing pipes? I can't reproduce it now.. weird. Even looked through the factorissimo code to see if there is an issue there, but it's pretty straightforward - maybe a factorio fluid rounding error on the transfer function? That same error that causes pipes to have 39.999 of a fluid instead of 40?? Wish I could help troubleshoot better.