If the IRA/SEP/SIMPLE box is marked on the Form 1099-R provided by the payer, the payer is indicating that the distribution from from an IRA, not from a 401(k). Perhaps you rolled a 401(k) into an IRA, in which case the money is now in an IRA, not in a 401(k), and is subject to IRA rules.
Nondeductible traditional IRA contributions were not permitted prior to 1987. Any nondeductible contributions made directly to the IRA for 1987 or later were required to have been reported on Form 8606 for the year for which the contribution was made. (Between 1987 and 2015, the maximum possible IRA contributions would have been $104,500, any portion of which could have been made as nondeductible contributions reported on Forms 8606).
Elective deferrals and employer contributions to your 401(k) were not after-tax contributions. Did you make other, after-tax contributions to a 401(k) that were subsequently rolled over to the IRA and, if so, do you have documentation to support the amount of your after-tax 401(k) contributions?
