Transport Pipe System Help

[tetris0420]

I'm making a basic Chest>>Macerator>>Chest>>Electric Furnace>>Chest system for autosmelting ores. I have wooden transport pipes coming out of each piece, with a redstone engine connected to it, and cobblestone transport pipes running till the next piece. After each of the first two chests, I have loops in the system allowing for overflow ores/dusts to return to the chest and be recirculated. However, sometimes the dusts going into the Electric Furnace don't go there. They just turn in the pipe and go around the loop back into the chest, as if the Furnace didn't exist. This is with nothing in the Furnace, with no reason as far as I can tell for the Furnace to reject the dusts. I've looked around and can't find help specific to this problem, so any help making this system as efficient as possible would be greatly appreciated.

*Does the same thing for the Macerator, I just haven't realized it until now.

If this whole setup is stupid and won't work, please let me know this as well. I saw it used just fine from someone I'm subscribed to on Youtube, but I understand that there are possibly (and probably) better ways to achieve what I'm attempting.

Screenshot of the system, hope this helps clarify what I've tried to describe.

http://imgur.com/mzvFAcn