Minecraft – I have a problem with some Minecraft hoppers!

If you watch at about 2:50, you can see most of the left half of the circuit. The part for the stairs looks like it isn't shown very well but that is less important timing wise. Watch carefully over and over and see if you can replicate it this way. It looks like the repeaters for the middle activate and deactivate immediately. So the order (from a circuit standpoint) for both directions is M, L+R. This works for closing because the middle repeaters don't have anything to activate until the blocks are pushed into the middle. When opening, they will retract the middle immediately.

Breaking it down:

Opening

1. Middle repeaters deactivate (middle pistons retract)
2. Delay
3. Left and Right redstones deactivate (left and right pistons retract)

Closing

1. Middle repeaters activate (nothing happens because the middle pistons are not in position)
2. Delay
3. Left and Right redstones activate (left and right pistons extend)
4. Now the middle pistons have been pushed into position and are activated by the middle repeaters

This is essentially how Minecraft operates: when items spawn inside your crushing block, the game tries to move them somewhere valid. Any non-solid block, like slabs or stairs, that won't push items, also won't crush chickens. Double thick walls may help, but not guaranteed. The game will just try to push items harder.

The solution is to put some kind of non-full-height block above the hoppers. This way, chickens will still have their heads suffocated by a block above, but their legs and dropped items will be in a valid space above a lower block's surface. Hoppers suck items in from the whole block space above them, so that would not be a problem.

Testing indicates that the obvious choice of short block - the Slab - works perfectly.

Also check the list of block heights here: http://minecraft.gamepedia.com/Solid_block#Heights