Minecraft Version: 1.10.2
Inventory Tweaks Version: 1.61-58
Forge Version: 12.18.1.2011
Java Runtime: OpenJDK JRE 8.u102-1
OS: Linux
Using default launcher and ingame settings, music turned off.

Steps to reproduce:

1. Open inventory
2. Add items to crafting area in non-optimal configuration (e.g. 3 planks above, 1 below, output sticks)
3. Middle click anywhere in crafting area
   The result is items returning to a stack in top left corner of crafting area.

Video: https://youtu.be/edvituRR6Ms

Same here with 1.12.2. How did you fix it?