Please ensure that you received the F428 Genie programmer with your upgrade. If not, please contact customer support. If so, please run the programmer. Instructions on using the Genie programmer are in the installation video at 16:05: 

https://www.youtube.com/watch?time_continue=967&v=6Ru9kGKcwek. The video is for the F-150, but the process is the same for all vehicles.