This might be part of the variability that people seem to be reporting regarding whether or not they get TSA Pre when you have Global Entry. You have to enter your Known Traveler Number into the information you give the airline for check-in and, depending on how you booked your trip (maybe through a place like Orbitz vs. directly with the airline), that information may not get all the way through to the airline. And, with some of the airline mergers, some of their computer systems aren't fully merged and information like this can get dropped. I'm pretty sure this happened to us once when we had a "mixed carrier trip" and didn't get TSA Pre on one leg.