Erroneously marking the IRA/SEP/SIMPLE box in TurboTax would likely cause TurboTax to treat the box 1 amount as the taxable amount. Otherwise it's likely that TurboTax is including only the box 2a amount on Form 1040 line 4b as the taxable amount. The amount in box 2a would generally be less than the box 1 amount only if the remainder of the box 1 amount was shown in box 5 or box 6.
