Most likely the problem is that my last name is hyphenated, but the airline systems don't accept hyphens. Even though my drivers license does not use the hypen, the passport might (haven't checked). The middle name is on the drivers license (and probably the passport). Without the hyphen and middle name in the reservation maybe Secure Flight just wasn't certain that I was the same person.

Maybe for the next trip I will try using just the middle initial.