When Left-shift clicking a stack of items it normally transfers from my inventory to a chest and vice-versa. 

Hardware

Keyboard

• Mac Mini

• External keyboard (Corsair K65)

However with a special BIOS switch on my keyboard I have left-shift click working for a second after pressing the key. So when timing the key and click right I can have a stack transfer. 

Wacom Tablet

• Wacom Intuos

However with my Wacom Tablet I can assing a key to Shift. When pressing that key and clicking with the tablet itself or the mouse the stack transfer works. 

Conclusion

So I think it is related to my keyboard. Although I only experience this issue with Minecraft. Hope this is fixable?