Are you saying that:

•Thermostat calls for heat.

•Flame ignites and fan runs as normal for some amount of time.

•Before the setpoint is reached, flame turns off but fan continues to run for some amount of time.

•Flame ignites again and continues to run until the setpoint is reached.

If true, this is a classic case of your furnace overheating. Check that the filter is clean and all of your supply and return vents are open and clear of obstructions.

If that isn't the problem, you may have a faulty temperature sensor in your furnace. It's also possible that your fan is not spinning fast enough for your system. Call an HVAC tech.