Issues with building a factory

[Chaqa]

I'm making a Block Breaker factory. It should be pretty simple, here's the layout:

3 retrievers connected to a master pipe system which is connected to all my chests.

Retriever 1 pulls sticks and iron for an iron pickaxe.

Retriever 2 pulls cobblestone and redstone

Retriever 3 pulls the items for a piston (redstone, cobble, iron, wood)

All 3 Retrievers are connected to a Retrievulator (to fix the issue of multiple retrievers not accepting the same item), which is then connected to an Automatic Crafting Table Mk2.

After Retrievers 1 and 3 make their thing it is pumped back into Retriever 2's crafting table.

All 3 are being pulled from by a filter, all 3 on the same signal (redstone tube and jacketed wire being used).

It works fine for a bit, but then the filters get stuck on. They won't work, the red line is there, and they are in the "doing something" phase... but never turn off.

Any ideas?

[Chaqa]

There you go for an image. I tested it in single player and multi player, same issue.

Thoughts?