If I use ctrl+shift+click to move all items of a type, it does not work unless that same item is also in the first slot of the inventory.

Some pictures to help clarify:
Moving all the coal to the player inventory will work, regardless of which stack of coal I use the shortcut on, as there is coal in the first slot of the chest. This would still work if the first slot only had one coal in it.

But now it won't, as there is a different item in the first slot; in this case, arrows. It also would not work if the slot the arrows are in was empty.

I have a few ideas what might be wrong, so I'll clone your repo and see if I can get it working myself.

Version info:
Minecraft 1.8
Forge 11.14.1.1419
Inventory Tweaks 1.59 and 1.60-dev-13