I've seen other posts about this, but they seem to have been resolved a long time ago even though I'm having the same issue has them. Simply put the shift+double click doesn't register the way it should. Whenever I do this on a stack it will instantly move it to my inventory so the second click will be on an open space and not move all stacks of that item. 

I'm not inexperienced at double clicking or anything of the sort I tested my speed and I can double click in .06-.13 seconds. Also it seems like having an item picked up by your mouse resolves this issue. The first click will move the item to my inventory and the second will hit the now open space, but it will still register this has a proper double click and move all stacks to my inventory.

It seems like minecraft moves the item instantly (you can still do it without an item in your hand but it seems impossible) but if you have a item grabbed it registers the transferred item has still in that space meaning you have a larger window for the double click.

I've been able to reproduce this in single player and multiplayer both acting the exact same way.