So to elaborate, I run a 2x server. Stack sizes in furnaces and TCs are 2x. Last week when you put items into the furnace they did stack to 2x. Now that I have made furnace splitter only avalible to a particular oxide group with proper perms, ONLY the ore will not stack to 2x with furnace splitter on. The wood stacks to 2x, 2000 wood. With furnace splitter off, the ore will stack to 2x, 2000 ore. With furnace splitter on the ore will NOT stack to 2x, 2000 ore. Any idea what might be going on here? Obviously from what I've said, it does suggest that furnace splitter specifiacally is disallowing my stacks to operate as normal. 

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.