I will tell you about a problem that happened to me and how I solved it. I was using Stack Size Controller on my server (eg: stackall 1000). Later I added Furnace Splitter to my server. However Furnace Splitter did not work in the small oven. I had to set the value to 2 instead of 3 for it to work. As a solution, after installing Furnace Splitter, you need to type stackall 1000 from the console again.