How come the temperature is sometimes not maintained?
If this is indeed two independent systems in one house (as it sounds like it is), the symptom you describe actually sounds like a common furnace problem, and you happen to have both doing it at the same time.

Flame sensor problem (I've had this happen myself)
The flame sensor is a usually L-shaped piece of metal that literally sits in the path of the flames, and detects their presence. It is a safety shut-off feature so if there are no flames, it turns the gas off. It gets dirty over time, and at the beginning will happen only occasionally, and will gradually happen more frequently as it gets dirtier. Cleaning it with some steel wool once a year will usually solve the problem. It is usually connected to the control board using a white high-temperature wire.

Igniter problem
Could be a bad igniter, which will cause the gas not to ignite at all. This could happen intermittently.

Exhaust blocked/backflow
There are sensors to detect when exhaust gas isn't being vented properly, so if your chimney or vent is slow or clogged, it may be causing this sensor to trip and shut off the furnace. This is less likely to be an intermittent problem, but is worth checking out.


In all cases, when there is a problem, the furnace will not try to start again until you cycle the control signal on the thermostat or cycle the power to the furnace itself.