Had same problem for a while. Delta Check-in folks suggested getting a "Redress Number" . A few weeks later got the Redress Number from Homeland Security, entered it into my Skymiles account and Lo and Behold... no more passport or ID verification problems upon check-in time. Might want to go on the Dept of Homeland Security website and check it out. Worked for me if you are having these issues...

https://www.dhs.gov/redress-control-numbers