It sounds to me like you have an air flow problem. This is pretty easy to figure out. Use a digital thermometer. Take a temp reading at the return air grill, then take one at the closest supply register to the furnace. Subtract the two temps from each other. If you have less than 16deg and more than 22deg difference. You will need to have the blower speed set. If you have a good HVAC company, they will be able to calculate and set this for you.
Good luck, let me know if I can help you in the future