On my 2nd character all runes need 2 instead of 1 rune per use. So 2x rune of shattering to shatter an item, 2x discovery to transform 1 item to a unique. Its not a visual bug, reloading doesnt change the amount I have left or the bug, on my main its also still 1 per use.
EDIT: Creating a new character still has this bug, tried it at level 2 on a fresh rogue and mage.