When the furnace sits all night @ 68 and then in the am I turn up the thermostat to say 71. The burners start to fire and then shut right off, they run no more than 10 seconds. Then the blower comes on and the burners start firing again. Then they shut off again, its an on and off again cycle every 10-12 seconds for hours until the house heats up. I am trying to figure out if this could be caused by the thermostat.

Start by cleaning the flame sensor with sand paper or replace the sensor.