Well, I duno if this is rly a bug but there is the following problem:

When I want to have some e. g. Bedrockium Drums, which needs a loot of cobble,
then the Ender Chest won't let the cobble trough if it's not a compleat stack of 64
cobble at the first place and I don't have the time to stand near the chest to sort
them correctly.

Q: Can it be that this cames from the Supplier Module MK2 which is in a Chassis MK4?
A: If so, pls change this to a simply output of the item also if it's not a full stack (16 or 64).

This is needed if I request some items wichs needs more steps to be completed because
my crafting setup is made over subsys (one for raw material converting (e. g. ingots to
blocks, wood to wooden planks, ...), one for tier 1, one for tier 2 and so on. So it can be happen, that one crafting order will go trough 2 or more subsys to be completed and if then the above "bug" happends the crafting process will be corrupted instandly, which is very bad :/ ...

Hope that you can fix this.

I don't really understand that.
What pipes do you have on all ends of the ender chests? How are they configured?

There is a Pipe called Logistics Inventory System Connector which connects to different LP-Sys to one system.

Now, if I request any Item it is transfered from LP-Sys-1 to LP-Sys-2, if it's not greater then one stack.
But if it's greater as one stack, e. g. 190 cobble, then it can be that I don't get all of them because the first place in the enderchest isn't a full stack. It seem that the Provider Module MK2 is also affected because it's better as the normal Provider Module and if I'm right the MK2 pulls out one compleat stack if requested more than one stack of the requested item.

Only card in the Inventory System Connector Pipe are the Logistics Item Card to connect two systems to each other, not more and not less.

Hope, that this description is better as the first one.

@chaos234 one picture says more than thousands of words. If you have a problem similar to this, things can go better if you post some pictures (I strongly recommend imgur because its album capabilities). Just FYI.

I strongly recommend GitHub. You can simply drag & drop your image file into the comment field.

I very like GH Issues image support, however it's not the best if you have to take more images and explain them. Imgur provides a bit cleaner oversight for the album and makes clear what description comes to which picture.