Did you perhaps also mark the maximize box for an individual 401(k)? If you were under age 50 in 2016, a maximum individual 401(k) contribution on about $44k of net profit would result in 60% going to the 401(k). If you were over age 50 in 2016, $58k of net profit would result in 60% going to the 401(k).
You might do best to delete your Keogh/SEP Wks and remark the SEP Maximize box. To delete the form, in online TurboTax click My Account -> Tools -> Delete a form, then click the Delete link next to Keogh/SEP Wks.
