Crafting something in a fabricator will replace the item in that slot with the first possible item (steel ingot -> steel block). It keeps the amount of material consistent.

I am unsure if this is a compatibility issue with Almost Unified

Ah, I think the way I have it set up, it recalculates the complete amount of material there and redistributes from scratch

What I could do instead is a more careful algorithm that tries not to bunch up the stacks you put in. i.e. It breaks apart / puts together just enough to take what it needs and no more