Furnace runs out of sequence?

It is a 2 stage gas furnace w/central air, the first fan comes on, the furnace ignites, the furnace runs for a short time then the flame stops the fan blower stops then the first fan that has been running the whole time, shuts off and starts rite back up and the whole thing starts over until the thermostat clicks when the temp is reached. It is heating the house fine but is running all the time.It is 3 yrs old and has never done this before