For some reason, when I select TAKE ALL everything ends up in my stash now, when before it used to go into the active character's inventory (which is empty, so it's not overflow). Any idea what's wrong and how to fix it?

Happens to me too, not a clue.

When you are in the menu where you pick things up. Middle of the window for it, there is a line with your parties character portraits, with a chest image/icon to the left of them. Select the image of the character you want to pick up, then double click the item of choice. It should zip into their pack. 

Same works for stash. If you hit the button above the chest, it just takes everything and dumps it into whichever of those icons is highlighted at the time. Whether its the chest, your PC, or one of your companions. 

Thanks, just noticed the same thing. Wonder how it got toggled to the chest in the first place...