I am automating with some cells, using item pipes, slot locking and configurable chests. However, I noticed some weirdness with my system, certain things were not crafting and then figured out it was because the pipes were not pulling from all slots of the configurable chest.

I then cutoff the flow of iron plates to the configurable chest, and noticed that gears stopped crafting, because the other 2 slots that I had plates in were not being pulled from. Screenshot explains it. I also attached a forced crash report for all the mod info.

As soon as I moved some of the plates to the top slot, gears began crafting again until that slot was used up.

https://pastebin.com/r672cXuQ

Items are being moved from the chest to the chest directly, which is why the gears have a stack size of 48. (16 is inserted and extracted right away)
You can fix this by properly configuring the pipes.

Not sure what that means. Does that mean you cannot use the I/O feature, but have to put in separate push and pull pipes?

Also, why would the pipe pull gears from the chest? There is nothing but the chest itself requiring gears. If that is the case, why are the plates not getting pulled and put back into the chest? Throughput limit?

You can use the I/O feature if you correctly set up the priorities for example, otherwise yeah you need separate pipes.

It tries to extract from each slot in order, and gears are the first non-empty slot whose contents can be moved somewhere else.

Another example. Polarizer not getting neodymium. When I took this screenshot, none of the machines were running.

Tried setting the input priority to 10 on the pipe, did not fix the issue

Item pipe in the configurable chest is set to 0. Tried adjusting the extract priority down, up. Nothing. Finally gave up and had to run a separate pipe. Also, the same thing was happening with the stainless steel ingots going into a compressor. They would not pull and I had to run a separate pipe. Also, much of the inventory was already crafted before I put it in the chest. I was trying to create a cell instead of a bunch of machines in different areas.

I have tried numerous combinations of priorities and it just does not work and maybe I am just doing something wrong. Here are some screens.
First one shows assembler running out of inductors.

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Second one shows the pipe into the assembler set with an insert priority of 2

Third one shows configurable chest with crafting components and only the one slot of inductors is being pulled from

The pipe coming out of the configurable chest was set to the default. I then tried changing the extract priority on the pipe coming out of the configurable chest to -10, no change. None of the inductors from the other slots got pulled. So, what do I have set wrong?

Make sure that the insert priority of the configurable chest is lower than that of the target.

I will investigate this further.