Thank you for the additional info, was able to locate the issue after knowing which mod causes the issue. It's a very annoying set of circumstances; EV Refining turns every furnace from a furnace type to an assembling-machine type entity, which messes with the detection logic being used by this mod, running during final-fixes, which (depending on the load order) happens exactly in between when I create the mini furnace, and when I need to check for the mini furnace, which is no longer a furnace type entity.
There is technically a reason for it, since they have a coal furnace recipe added, that would start cooking the fuel when there's an input shortage. There's probably a better solution to this problem, like.. adding an intermediate crafting recipe to turn the coal into an item that can be cooked in a furnace, but that's just my opinion.
Should be fixed in v9.3.2