There is a small issue with the shift-click behavior button. When I set it to double click to quick switch between the modes and I hold down the shift button to move items quickly it keeps switching as if I was double tapping my shift button. This then makes it appear that all items have moved over but if you close the inventory there are a few stacks left that didn't move because of the "Glitching" shift-click state.

This is actually caused by a sneaky vanilla bug, that I noticed I think around the 1.11 port. From my notes:
- Vanilla bug: Keyboard.enableRepeatEvents() is true after a world load, if Realms notifications are on => HandyBag double-tap-shift status flickers if shift is held down

If I remember right, it will be fixed by just opening and closing the chat once after loading into a world. And disabling the Realms notifications should stop it from happening. I think I could also fix it by just disabling the repeat events when the Handy Bag GUI is opened... I'll probably add that for the next version.

Ah yes that seems to fix the problem. Thanks! And thanks for making a nice mod :)