I noticed a burning smell coming out of the air ducts. We turned the heat off. When we tried to turn the heat back on the heat ignited in the furnace but the blower never turned on after about 1-2 minutes the heat turned off. We noticed the burning smell again. If I turn the blower to on, on the t-stat and then turn the heat on everything works fine, the heat turns on and the blower pushes the heat through. It just won't come on with the heater when the t-stat is set on automatic.

I would inspect the unit or have a professional on site service look to see where the smell is from. It is a good possibility that whatever controls the fan in the heat mode is defective causing the odor.