I could see it going either way. I plan to contact the enrollment center again prior to our next trip, or even drop in and pay them a visit. Assuming the agent was able to see her enrollment and fingerprint waiver, there must be a bug that's causing the kiosk to not recognize the enrollment when her passport is swiped, but their internal system seemed to believe she's enrolled.
In any case, when we come back from our next trip in March, we'll have a blue form in hand, just in case, but will try our due diligence with the kiosks first.
FWIW, both agents (both at the GE "X" desk and at customs) at SEA were understanding and helpful in moving us along. We were both dead tired, so obviously weren't at our best, so they deserve some credit.