Really, and that is how it's always been. Any time stackable items are placed into an inventory (whether it be you or your retainers), the game automatically searches for a partial stack of the same item and quality and tops off the first partial stack it finds before overflowing into the next partial stack it finds (and subsequently any other partial stacks in turn) before creating a new stack.
It is only when something is removed from a stack (such as using them, purposely splitting them or withdrawing them into another inventory) or there are not enough things to make a full stack that you create a partial stack.
The only exception that I've seen to this is FC chest storage. That interface is incredibly rigid and it doesn't search for automatic stacking of the items you place within. You can however still manually place one partial stack on top of another to top it off, you just have to find them yourself first.
Edit: Oh, and the players who came over from 1.xx, a lot of them initially had extra partial stacks when they came to the new version of the game. This was partially because of an increase in stack size (a lot of old items had stack limits of 12, later increased to 99), partially because some things were just strangely transferred.
