Mass storage takes a long time to accumulate heat. If the house has been shut down with no heat running through the mass then it is probably cold. I would also be concerned that the pellet stove might not be providing enough heat to the chimney. Wood stoves are less efficient ( for the most part) but put more heat into the chimney, if the system was designed for a wood stove then the pellet stove might be part of the problem. If the air coming out of the ducts is cold, then I would shut it down till summer. You may want to turn it on intermittently, just to make sure the air doesn't stagnate in the system.
This summer, when the house is hot run the fan. This will cool the house and over time warm the mass. Mass storage systems don't just turn on and off like a normal heating and cooling system. Thay act as a thermal flywheel, in that the system stores and releases energy at a very slow rate typically over several months of operation. If sized properly to your house, cimate and heat loss and gain calculations a system like this could provide a good protion of your cooling load. While doing this it will store the heat in the mass and over the course of the summer should raise the temperature of the mass. I think you will find that the mass will help more for cooling than heating, although it should moderate the house well into the fall.
I'm with Jonr on this one for now, if the house is hot run the fan, if cool air is coming out of the vents then the system is working. Setting it up on a thermostat might help but if the house is calling for heat and the system isn't providing any, the temps in the house will drop as a result and the thermostat won't turn off and the system won't be supplying heat but actually removing it. I would recommend for now that you monitor the system for performance. This could be as simple as place a thermometer near the supply line or lines entering the house. Turn the fan on and see if the air coming out of the system is doing what you want. If your in heating mode and the air coming out is colder than desired turn the fan off and probably wait till summer. Once the summer months approach and the house requires cooling, turn the fan back on and see what happens. Once again monitor the temps near the supply lines. Once the air coming out of the system isn't cooling the house turn it back off. What ever the case I do not believe the fan was designed to run 24/7 and if your cooling the house when you need heat then it is definetly not working and should be truned off.
IMHO I do not beleive that you will see any benefit from this system until your home calls for cooling and you will most likely have to wait until summer months before running it. However I do believe that will also see some benefit in the fall months from the heat stored over the summer. I built an ICF house that also had some slabs creating a large thermal mass. The house was still cool from the mass effect into the begining of August and continued to warm into early September. It also moderated the temperature swings within the house into the winter months. From my observations of this house I beleive that the flywheel effect can take as long as 3-4 months to reverse cycle. This of course based on one specific house containing mass in a New England climate. Designed for passive solar gains, to a mass floor system, ICF walls and foundation, SIPS roof, High solar heat gain windows with shading/insulating system, radiant floor tied to a high efficiency on demand boiler. No cooling system was installed and the house did not experience overheating issues, except for a few hot days in August. I am sure the flywheel effect will be different from region to region, so there is no set answer as to the best use of such a system. It will most likely take some human intervention to operate this system, turn it on only when it is giving you the desired results, for cooling and heating. Occasionally operate the fan just to move the air but keeping this on 24/7 does not make sense if it isn't providing what you need.
Good luck, with what sounds like a one of a kind system.
Tom Pittsley
[email protected]www.eebt.org