The IRA/SEP/SIMPLE box being unmarked on the Form 1099-R provided by the payer simply means that the type of retirement account from which that RMD was made is some type of account other than a traditional IRA. For example, 401(k) plans and pension plans are not IRAs, so distributions from these would not have the IRA/SEP/SIMPLE box marked on any Forms 1099-R reporting distributions from these.
