HSA "deduction"--I already reported what is showing in box 12 on W-2 for tax-free employer contributions. Would this not include what I had payroll deducted?

Box 12 W is supposed to be the total that was deposited by your employer (their money and your pay deduction). They should reduce your wages reported in boxes 1, 3 and 5 by the amount contributed from your pay. They should not include in those boxes any amount they contributed.