Note: This is probably a duplicate of MC-6608, but that report doesn't have any information on how to reproduce the bug, so I posted this issue.

There are some cases where a hopper won't transfer items into a chest when it should be able to.

How to reproduce:
-Place down a chest block and a hopper that will transfer into the chest.
-Fill every slot of the chest with one diamond.
-Put an emerald into the first slot of the hopper.
-Put a stack of diamonds in the second slot of the hopper.

The emerald won't transfer to the chest because there are no open spots for it (which is expected), but the diamond does not transfer into the chest, even though there is plenty of space for it. I don't know if this is also intentional, but it's annoying when trying to sort items, it can cause the process to be slower.

You can see the bug in this video:
http://www.youtube.com/watch?v=mhJvcKnCZqs#at=232.5
He's making a simple sorter, but the gold ore in the hopper he has won't transfer until the diamond transfers completely.

This probably happens because of a check that sees if the first hopper item can be transferred into the chest, and if it can't, it doesn't bother trying to transfer any of the other items in the hopper.