I'm having the same problem
The last trip that I took, the TSApre was missing from my boarding pass. When I looked at my profile, the KTN field was blank. My GE was recently renewed, so I'm assuming that was the cause. I've popped the number back in and have my fingers crossed for my next trip.
The only other time I didn't have TSApre was when I booked a ticket over the phone with a Delta agent.