I managed to build 2 advanced smelters finally and started making some copper with it. For me also, 2 first batches of copper were fine, but the third ate my ore and charcoal. My ore slots were both 5/5 copper and fuel 4x charcoal. Aside from the 2 advanced ones, I also have 5 normal smelters that were loaded up at the same time.
Hopefully this gets sorted out soon 
EDIT: I tried also not moving the other advanced smelter and moving the other to a free spot and back and seeing if there was difference, however both smelters went like the one in the screenshot. I'm quessing I'm not getting my ingots this time either. The normal smelters are running this run again.
I always load up copper/ores first to every smelter then load fuel the next round and last round i start everything up.
EDIT 2: I tried adding copper ore while it was running and the earlier ores had disappeared. Interestingly, the first ore i put inside brought back the counter for the first slot, with the timer showing the correct amount of time left in the smelting process. Then I added 5 more (4 went to the first slot to fill it i quess) and the 5th ore brought back the timer and ore in the second slot. The same with the other smelter, added 6 copper ore in it and both slots were back in business.
I'll need around 3:50 to see if I get some ingots.