Maybe try this before call an HVAC Co.
Are that dampers you did locate for your main floor?
If so, damp those ones down a bit, this will effect air flow on your upper level. You can also adjust (close) the dampers in various Hot air vents on the main level. And leave your fan setting on your thermostat to "ON" not "AUTO", when the furnace fan is continuously blowing it will circulate the warm air throughout your house, also good for preventing moisture build up on windows.
Also, your thermostat location (likely on the main floor) has a lot to do with this. When your main floor has reached the desired temperature, the furnace will no longer call for heat.
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