My one furnace is in basement and second furnace is in the attic. It is 4 years old house. During very cold weather the attic furnace shuts off and it takes couple of hours to come on. Probably when the temp rises. How can I fix this problem? Is it the condensate line freezes and furnace shuts off?

Actually condensate freeze problems could be a problem. In cold climates with a well ventilated attic it is a known fact that freezing of the condensate line can be a problem. Usually in those areas a flexible style heater is wrapped around the condensate line and that is wrapped in insulation to help prevent this problem.

Another possible problem also exists with gas valves and related components. I the attic space is well ventilated in very cold areas the attic will reach almost the same temp as the outside especially in a newer home that has a very well insulated floor area in the attic. Manufactures of the gas valves and other components have a listed minimum temperature range that they will operate under. If the temp in the attic is below that temperature it is a good possibility that the gas valve will not activate thus no heating will happen from the attic unit until the attic warms up later in the day or week depending upon the outside temperature.

I always suggest you contact a professional for On Site consultation for these types problem since it is usually beyond the scope of the every day homeowner.

While I am not suggesting you do this the little story here is true and it happened to a friend of mine who lives in up state NY where it gets dag gone cold.

He had a similar problem as yours so I told him to install a 100 watt light bulb next to the gas valve on his unit. So he took a trouble lamp rated for a 100 watt bulb and hooked it up. Low and behold the no run when it was real cold problem went away. This situation was finally fixed when I found a similar gas valve for his unit that was rated for roof top furnace use. Roof top furnaces see very cold temperatures in the winter since they are outside on the roof plus the wind chill factor creates a very adverse condition for a gas valve to operate under.

In my area years ago we had a short but brutal temperature drop. All the commercial customers were calling saying the heat was out. I sent my guys out with a good old hand held propane torch and they warmed the gas valves up until the furnaces started to operate. I instructed them to tell the owners not to turn off the furnaces since they may not start again. I can just imagine how big there utility bills were but they had heat and no busted pipes.

As I mentioned contact your local trusted HVAC Company for the proper solution. In fact I would contact the company that installed your unit since they did not take this into consideration when doing the install.

There are other possibilities to this problem but temperature related failures usually effect the gas valves the most. Combustion fan motors can also have temperature related problems since they also have different operational temperature valves for different locations of install.