Hopper is losing items

I was making an auto smelter, but as I was hooking it up, I noticed the items were not being put into their carts. I was trying for ages, and lost a few items. 
I realised that the items going into the hopper and cart would disappear. I had removed and replaced them, but they still do not work. The upper one works perfectly, but the lower one just loses every item that goes in. 
I will attach an image. 

Lower hopper has the issue, the upper is fine...