Same Problem Here
My company also uses Concur, and my last two trips had the same problem. Booked via Concur to SWA, Known Traveler # in the booking, hit the SWA system as a redress #. Last occurrence was outbound on June 10, also happened on the June 3 outbound.
The SWA counter agent added my KT# and re-issued my boarding pass with pre-check.
Will be curious to see if the fix (referenced above) takes hold in July.