See attached save game. Disable editor mode to start. Save has a regular furnace that has the issue and a metal mixing furnace (like a furnace but can have a recipe set) that works as expected. Wood can both be used for fuel as well as being an ingredient for the recipe, turning it into coal. The metal mixing furnace loads 5 wood into the fuel slot then loads wood into the ingredient slot. The regular furnace will load 200 wood into the fuel slot before loading any into the ingredient slot.
Both of these were started at the same time. The metal mixing furnace has started making coal. The regular furnace won't start until it's fuel slot is full.
Additional information: this happens to the regular furnace even if you prime the furnace with a specific recipe so it shows up on alt-mode and on the map – the inserter will still fill the fuel slot before putting anything into the ingredient slot.
Thanks for the report. Issue is now fixed for 1.1.40.
Issue was due to different transfer implementation for furnaces which would always try to insert item with fuel value to the energy source first even when the energy source already had enough fuel. After this fix, furnace will behave the same as the assembling machine: transfer to fuel inventory will have priority when there are less than 5 items in fuel inventory and then it will become a fallback for remaining transfers.