WN participates in Pre-Check. It is a TSA-administered program and has nothing to do with your "status" with WN or any other carrier.
If you receive a BP without the Pre-Check logo, you may have been randomly or intentionally deselected or your passenger data may have been screwed up. WN can remove your KTN and then reenter it and you can try reprinting at the airport. If it still does not work, chalk it up to bad luck if it happens just this once. If it continues to happen, you may want to consider applying for a redress number.