For some extremely bizarre reason, when I input Cobblestone into my Vanilla Minecraft Furnace, when it is smelted with any fuel source, you cannot Shift-Click it into your inventory, but you can click it and drag it into your inventory. You get no exp from the smelting, If you have another one smelted and put upon the previous Stone, it disappears and only one Stone will be there in your inventory. If you put the Stone in your hand and try to place it or block it, it'll disappear. If you right click it a bunch, the block will disappear from your inventory. This has never happened for and I find it extremely bizarre, not sure at all what it causing this, I've destroyed the furnaces and placed it back down, replaced the fuel sources, nothing. I'm using Vanilla stone and cobble on a side-note.
have you put a ticket in for this issue Omega. that seems like it may be an Admin issue to get resolved. or what you can do is a force update from the launcher to see if that helps