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Get your taxes done using TurboTax
The only way that I've been able to cause TurboTax to treat a box-1 amount as a subtraction from income on a Maryland tax return is to indicate when entering the particular Form 1099-INT into TurboTax that Maryland does not tax all of this income. It seems that it should be possible to rectify this by deleting and reentering the Form 1099-INT that has the interest shown in box 1 and not box 3.
Still, it's possible that some amount got entered directly on the related worksheet on MD Form 502SU. It seems that this amount can be eliminated either by simply deleting the Form 502SU and allowing it to regenerate, or by editing the Form 1099-INT, marking the box-1 amount as not taxable to MD, then editing again to remove that indication. I would try the latter first since deleting the Form 502SU might necessitate going back and reentering other subtractions from income that might not regenerate.