TL;DR:
file: xander-mod_3.4.4\lists\entities.lua
line: 334
base_level = -1,
I think I figured it out. Note: Not tested. Please respond here if this works.
One of the inputs on the electrolyzer is setup incorrectly to have a "base level" of 1 instead of -1
My cursory investigation into fluid boxes indicates that the base level needs to be low enough so that fluids can flow in. My guess is that pipes have a base level of 0 and a height of 1, so they can't get up over the base level. In a way, the input is acting like an output. Sort of.
Solution:
In \lists\entities.lua
find the entry for electrolyzer-1
. Find the fluid_boxes
and set each one marked production_type = "input"
to have base_level = -1
.
Make sure you leave the ouputs to +1 though.