I am glad that I am not alone in having problems. This is happening to me domestically. The last three times were EWR-MSA, MSA-EWR in December and tomorrow EWR-SAN.
My boarding card is not marked for secondary inspection and when I go to print it out at an airport kiosk, I'm never directed to any CO agent to check my ID if no bag check-in.
I travel on a New Jersey drivers license domestically and internationally exit/enter the US on my American passport. The system has this info on file, so "knows" who I am.
The challenge is that nobody at CO can tell me what the problem is or how/if it can be fixed.