I had been through the same thing as you and spent weeks researching. Someone mentioned an overflow problem and I for get who made the Vidio but there is a salusion in a Visio called 1.6.1 item sorter overflow protector. Honestly I found it to be to complex, expensive and big. When the chest becomes full the hopper does to which in turn powers it on to give off a pulse. The torch that you place under it actually powers it off but when it's full the hopper turns off that torch and in turn breaks the circuit and then the hopper system before it breaks as well and stops sorting. If you put a lot of items in to sort then this can jam your system up quite a few chests. Separating your chests kind of helps, or you can use the expensive overflow protector, or did what I did and take cobblestone/dirt/redstone/even sand out of the system. The reason for the sorter for me was mainly to be able to find the abundance of random items I had easier anyways so the last was the easiestAlso I did need to rebuild all my broken circuits from scratch to reset them.
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