If the IRA/SEP/SIMPLE box is marked on a code-G Form 1099-R, the form is reporting a direct rollover from a traditional IRA to the traditional account in an employer plan like a 401(k), not the other way around. If the rollover was indeed from a traditional account in a 401(k) to a Roth IRA and the 401(k) plan marked the IRA/SEP/SIMPLE box, contact the 401(k) plan to have them correct the form by unmarking the IRA/SEP/SIMPLE box. A 401(k) plan is never permitted to mark the IRA/SEP/SIMPLE box.
For a direct rollover from the traditional account in a 401(k) to a Roth IRA, the after-tax amount should be present in box 5 of the Form 1099-R provided by the payer.
