I'm currently playing with Warptorio2 mod. I'm not sure if the problem occurs in vanilla, but I'd bet it's independent of the mod.
Splitter (one tile below the character) seems to prefer the bottom input instead of taking items from both items alternately. I tried to fix it by removing the splitter and placing it again. Then it worked as expected for a short amount of time, but quickly started to switch to prefer the bottom input. The entire change took 1-2 seconds.

