Note: If this was an intentional change, than please ignore this report.
Let me set up the scene to make things simpler. I have four chests stacked on top of each other, each with a hopper leading into it through the back, with the hoppers being stacked on top of each other. Normal hopper behavior dictates that all items, no matter how many enter the hoppers at once, are moved to the hopper at the bottom and are then moved to the connected chest. Currently, however, throwing in more than one item at a time makes half the items travel to the bottom, as they should, but the other half are moved into the top most chest.