This is especially prominent with the Ultimate Furnace due to its super fast nature and meaning that if it is not constantly on then it turns on/off a lot.

First noticed on 1.3.9, but still occurring on 1.4.1a (on 1.10.2)

Graph of Alt+F3 showing the fps spikes:

What fuel are you using that makes it stop working so quickly?

Its not the fuel running out, but I am using an ExtraUtils 2 Heating Coil, its the fact I'm piping lots of different things to smelt. Although, I'm having second thoughts if its actually the furnaces causing the spikes. I was quite confident it was the furnaces but it might be Ender IO conduits. I will try to see if it is actually the furnaces and comment back later. I will close this issue for now and re-open if it is the furnaces. Sorry for any problems.