Industrial Foregoing Version: 2.2.2-28d4a81
Forge: 31.1.41

You are maybe aware, but shift clicking items into machines has some very "odd" behaviour. Sorry for being so vague, but really sometimes it works, sometimes it doesn't, haven't seen a specific pattern yet. Especially for upgrades it doesn't seem to work, same goes for shift clicking items out of machines into the inventory.