You might check and see if somehow it got turned off in your driver information center. Just scroll down and make sure it's enabled. If not then it might need to be reprogrammed.
I tried to remote start the car after an oil change with the hood up, and the lights flash but it didn't start, closed the hood and it worked fine. Not saying that for sure the problem but I wouldn't be surprised.Hood switch could be the problem, it can't be jumped, it's a Halls Effect Sensor.