What should I look for if the furnace is coming on but the blower isn't? The small box has a red light flashing. The bigger box is flashing a green light, three flashes at a time.

Check for power to the motor, check the capacitor, and if you have a good cap and power to the fan, then you need a new motor. The blinks are most likely indicating an open limit, due to the furnace overheating because the blower is not running.

So, to sum up, if the blower has power, and the cap is good, then you need a new motor.