Happened to me, check drivers side plug where the three wires plug into the factory turn on connectors.... That's what happened to me, I had to fix the wires around a few times and then it works....
Hope this helps!!!
CAI, SF3/X3 Tuner, 4.10 Gears, Auburn lim-slip
GT4 Rims (Summer), Stock Rims (Winter)
2 Subs, New speakers all around
1 Great Car 1 Happy Kid
July '12 Mustang of the Month