I have RedstoneSpire's 5200 iron/hr iron farm on my CraftBukkit 1.8.8 server. It is started by a "hopper-clock pulse extender" with two facing hoppers containing 128 items. The hoppers are normally stopped (no items transferring) until a reset signal is applied which extends the sticky piston (the other piston is a regular piston).

Sometimes after reloading the chunk, the reset signal no longer causes the sticky piston to extend. The only way to restart the clock is to remove and replace the items. The reset signal should always cause the sticky piston to extend.

RedstoneSpire's iron farm: https://www.youtube.com/watch?v=sNZsP36hqxk
Sample hopper-clock pulse extender: http://minecraft.gamepedia.com/Pulse_circuit#Pulse_extender