Have the builder check it out cause it can be a problem. You probably quit using the furnace. Part of the draft problem in the vent is that as long as it stays warm, it will updraft. With the furnace off, and the water heater not heating enough to keep the vent warm, then you have the problem you have.
Of course like Jay said, the fresh air intake could be part of the problem and maybe an elbow or something may help solve the problem. Talk to the builder though.