From patch note 1.0.4
"UI
General
Changed the functionality of auto-stacking in guild banks. You will now have to stack items in your inventory before placing them in the guild bank."
Auto-stacking in guild banks never worked for me (or at least not for every item) but i think it's a feature they should add, not remove (or at least make it possible with a button).
Is it possible to make an addon that performs the auto-stack in guild bank?
Maybe performing a withdraw - stack - deposit - next item....