How can we get the temperature balanced in a dual zone house?
Is the house drafty? We had a similar issue with the first floor, the heat always turned on and off. I first replaced the old thermostats for new ones, but still no affect. 
What it came down to was our old windows created a lot of drafts and the door to the outside was right next to the thermostat, so every time we opened the door to go outside and cold air entered it turned back on. 

I would check the locations of the thermostats, and potential influences to cause the temperature around them to be effected.  

Also try adjusting your thermostat to reflect the overall temperatures of each floor. 
With our home upstairs is always 4 degrees hotter, and so if we set the 2nd floor to 65 we set the 1rst floor to 61.