Guys I already know what causes the glitch. And it isn't just Classic. It is also on Ulti. I would know. I am on 5th place on the Ulti leaderboards. I play a lot. Anyways the way it happens is when you open the enderchest, add an item and as soon as it is placed you exit the enderchest. Meaning you open it... look in for a while, "Hold Shift" to quickly place an item than a second after placing, exit the chest. By doing that there is a high chance of it vanishing. No idea what could cause that to happen. But yes this is annoying.