Likely you have client who has opened a Roth 401K within the last 5 years.  So the difference between box 1 and box 2a if the non-taxable contribution.  Is the difference (basis) included in box 5?

Reguardless in order to get the amount in box 2a to show as taxable you have to pretend to be Russian.  Use B7 bomber check button 3/4 of the way down the worksheet in the rollover section.  Program will then only include amount not eligible to transfer to new company as income.