Yeah the first one is TileEntity Data being wonky, but this Data became wonky, because of the Block ID Map being completely out of whack thanks to that Forge Bug.
I will make double sure the Y Coord of my TileEntities is not smaller than 0 whenever i use the setTileEntity call, because I indeed did not know before where exactly this Issue came from. But I highly doubt I ever called it with a negative Y value.