That code is indicating that the flaps inside the intake are not functioning properly. However you said you have the 3.5 Ecoboost correct? I don't believe that intake has IMRC but I could be wrong. When I removed mine and painted it I don't recall seeing anything like that. The non ecoboost 3.5 uses a plastic intake runner which may have this IMRC system.
Is your intake plastic or aluminum (Ecoboost)? I would check the wiring harnesses around the intake. What did you use to scan the vehicle?