I have a 95% efficient tempstar furnace model N9MSE that my wife and I purchased 9 months ago. It turns on and cycles 1 or 2 times then shuts off and flashes 3 times. I've checked the airflow, and drains, and everything seems to be clear. I also noticed that if it is at temp in the house, it can maintain it, but shuts down when it needs to continually try to warm the house.

Check the error codes, usually inside the air handler door or on the control panel.