Issue description:
This happens on RFTools Modular Storage. When I put items inside, it counts the number of used stack slots. When I pull something out by clicking on the item and putting it into my inventory, it decreases the amount of slots used when hovering over the machine outside, the indicator bar on the front of the machine shows the correct amount as well.
However, when I shift click on a stack, it puts it directly into my inventory, the number of used slots inside the machine is shown correctly, but the number of slots used outside the machine, both hovering and on the frontface don't decrease the amount for taking stacks out. This leads to the machine now showing 347 of 300 slots used on a tier 3 storage card.

Steps to reproduce:
Put items into a modular storage unit or have them put in by a machine (in my case a void ore miner from Environmental Tech), then pull them out by shift+left clicking on them.

Versions:

• Minecraft: 1.12.2
• Forge: 14.23.5.2847
• CompatLayer (only if on Minecraft 1.10 or 1.11):
• McJtyLib: 3.5.4 (latest)
• RFTools: 772 (latest)

Possibly incompatible mods and versions:

Relevant logs, if any: