Are you using a paper or mobile BP? Sometimes I don't see Precheck on the paper (such as when going from international>domestic>domestic and the initial leg was on a partner), but the mobile BP will have it.
If it's super important to you, you can ask the counter agent to check if the KTN is applied, and if not they can reapply it and reprint a BP.
As others have mentioned, I see this issue sometimes when booking through a TA like AmEx travel desk when I hit some limitation in Concur.