TurboTax shows our AGI as total income despite 401(k) contributions, with no adjustment. I verified W-2 entries, including Box 12. How can we fix this?

The 401K in W2 box 12 have already been deducted from the wages in box 1 and you can’t deduct them again.   See box 1 should be less than boxes 3 & 5.  Ask your employer.