We also had this issue. I had to type in the number when I booked the companion fare, the system didn't pull it from the profile automatically even though it was stored there. The KTN in the profile worked for her own original bookings, but not companion bookings by me.
The companion can also call and have it added separately anytime, or add it at the airport if you are checking bags anyway and reprint/download the boarding pass.
Home airport MDW, frequent visitor to MCO to see the mouse.
