To replicate :-
1) Put down 3 large storage boxes
2) Make 2 pipes from one storage box to the 2 other storage boxes, so one box will split it contents into 2
3) Upgrade pipes to HQM
4) Put 500 smoke grenades into the first storage box
You would expect 250 smoke grenades in the 2 other boxes after it has finished. Instead you get 450 and 50.
It seems one of the boxes gets nothing put into it until there is 100 smoke grenades left in the first box, and then that 100 is split evenly between the two boxes (50 each). Putting in just 100 smoke grenades evenly splits 50 into each box so the problem only occurs when there are more smoke grenades in there than can be evenly split in a single cycle.
The same problem occurs if you split into 2 , 3, 4 , 5 or 6 boxes. Only one box gets filled until the very last stack.