I don't know what happened with the hotfix, but several things has changed. This is in a new game, Explorer mode on PC.
Suddenly, individual items don't stack. You will find 3 arrow shafts that won't stack with other arrow shafts, or a single ruby that won't stack with others, despite having the same values.
Item drops and treasure is still messed up. The problem I described in my list on page 7 of this thread, persists: You can find three identical magic items in the same area. I just found two similar daggers in the same room.
Also, and this is probably related to the problem above, the "item of the week"-bug keeps on going. Example: In my current game, every single merchant stacks a copious supply of yellow dye. So far, no other color has been available. In my first playthrough, I didn't find a single water balloon or oil flask, now they're everywhere, usually in stacks.
I'm no expert, but I think there is something fundamentally wrong in how items are generated, which affects a lot of situations throughout the game.