I've run into the same problem. First thing I learned is that I always have to manually add my trusted traveler number to tickets booked through the corporate site, even though it's in my profile. But even then, sometimes the BP prints without it. I've tried calling, but apparently the only way to fix it is to have CS at the airport manually check you out and then re-check in, which kind of defeats the purpose of having pre-check so you can get through the airport quickly.

The new site may be pretty, but I'd like it better if they'd spent the IT time and dollars making web services work properly instead of on cosmetics.