This sounds like a glitch. If your e-ticket was booked using your DL profile and your KTN is properly in your profile, there should not be an issue unless there is a problem of a larger nature.
Go into your DL profile, remove your KTN and save. Close the browser. Then go back in and enter your KTN and save. Then double-check that the name in your profile matches whichever TTP, GE or Pre-Check you use and that your tickets are booked under your name as it appears in your profile.
While unstated in the OP, it appears that when the KTN is attached to the PNR, he does get Pre-Check, so it seems unlikely that TSA has identified a security-related issue.