If the burners turn off while the fan is running could be caused by two things I can think of, one is that the limit is set too low, therefore the limit breaks before the house is warm. Another things is about the fan switch spinning when the burners turn off, Could some outside air be getting into the return air duct, if so this would make the fan cut off and 90 degrees F and then come back on when the burners get the temp back to the temp set on fan on setting. The 90 degree setting is a little low for the fan off setting, I would rather see something like 105 degrees.