Stack conflict

It appears that items crafted in the mixing table are having issues stacking with items normally crafted.
Example is gunpowder.
You can stack them while the item is crafting, Though it will create a separate stack smaller stack and the crafted items will bounce between each stack as you combine them.
After vanilla crafting is done, stacking is impossible..
This is only an issue if running a stack manager. Currently I am using Loot Table & Stacksize GUI (Resource stacks are set to 100k)

I tried this with the umod version of Stack Modifier as well and had the same result.

I'm currently running ConsumableEffects, CustomMixingTable, ExtraGatherBonuses (your version), ImageLibrary, StackModifier/Loottable and Whitelist

Edit:The error is being replicated on my test server after pulling all other plugins, using the ones listed above, and starting back up.

Could you send me video clip of that issue please?

So after giving it another go I found that quick looting will cause them to stack. But trying to manually stack is still not possible.