Try disabling LLC and see if that changes the readings CPU-Z is giving you. Also, I'm guessing this isn't the case, but you haven't accidentally switched the CPU overvolt jumper on the bottom right of the board, have you (see eg. page 1-20 of your manual)?

Have the same setup (5960X and X99 Deluxe) on its way to me, should be arriving late this week, so will be able to comment if I see the same behaviour then.