Initial Conditions of FAST versus Simulink

I have implemented the controller for the NREL 5 MW in simulink and I am getting the same steady state outputs but the initial start up portion of the simulation, approximately 20-30 seconds depending on input type, is slightly different. It seems that the initial conditions are affecting the controller. What executes first when running FAST from simulink? Does the S-function execute first or does all of the control logic execute?