Picture is a better representation of what problem I'm having. Comparator does not output a signal from the stacked hopper while items are travelling through unless a redstone signal is active near it but not powering the hopper.
The left side has no output from the comparator while the items are moving. The right side does receive output because of an indirect redstone signal. This make no sense - almost as if the redstone is slowing the item down enough for the comparator to make a signal. Note that the redstone signal does not close the hopper.
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Confirmed.
Tip: Put a chest below the hopper to probe.
Maybe the pulse is too short if the hopper pushes to the hopper below and the hopper below pulls from it.
Duplicate of MC-8457.
This is not a duplicate of MC-8457. Based on the OP's comments, the comparator isn't drawing a signal if a chunk is unloaded then reloaded also they made a comment about direction the comparator faces. I will post my info there. But the bug I reported is directly related to the hopper being semi-powered.
On the left items are traveling twice as fast as on the right, no time for the comparator to update.
This is not resolved. This is still a bug. A pulse cannot be pulled from a vertical hopper stack unless a a redstone block is placed below the comparator.
The right side does receive output because of an indirect redstone signal. This make no sense - almost as if the redstone is slowing the item down enough for the comparator to make a signal. Note that the redstone signal does not close the hopper.
The redstone signal in the example on the right do power a hopper. Your redstone dust power the block on which it's placed, which in return power the hopper next to it, blocking it. It does slow down the item, letting the time for the comparator to update its output. Output which isn't generated by an "indirect redstone signal", as you described, but by the comparator testing the content of the hopper, as expected.
No the reason it doesn't make sense is because when hoppers are place horizontally a signal can be emitted but not vertically. Placing a redstone block on the hopper shouldn't slow down the items, it should either have no effect or stop them completely. I've given up trying to make mods understand that this is a bug. I just have to unnecessarily include a redstone block on every chain now.
A hopper push and pull. They can only pull from containers above them.
A horizontal chain of hopper will carry item mush, mush slower than a vertical one, as the hoppers in it will only push items, but a hopper in a vertical one will both pull them from the container above and push them in the container they're connected to.
As to why items will not stay in the blocked hopper is because this blocked hopper will neither pull or push items, but other non blocked hoppers around it are still capable of pushing items into it or pulling them from it. You need to block two consecutive vertical hoppers if you want to stop that chain, preventing the first one from pushing items into the next one, and the next one from pulling them from the first one.
It totally makes sense once you've understood how hoppers work. This is a completely intended, normal and expectable behaviour.
Did a bit more testing and there has to be 2 hoppers below the powered block for the item to pass.