A little messing around I was doing. It looks like the issue is coming from the position of the items on the output belt to me. (please don't mind the mods, this does the exact same thing in vanilla)

I will have some time to fix this soon, in the meantime it should work if you remove autofill, save the game, then re-add autofill

Just to let you know, this does not work.

Love ths mod by the way, and look forward to being able to use it again :D, but I know how RL obligations can be, so will ...