If you have the type that doesn't bring in combustion air that is the problem. When the furnace or WH turn on that causes negative air pressure and it will pull in through the easyest pathway which must be near the termination points, perhaps the holes cut for the exaust pipeing.
See if there is a place that you can add another peice of combustion air flue pipe, that is not near the furnace and WH termination and run it to or as close as possible to the WH and furnace. 6" is normaly used.
Also look near the WH and furnace termination points, inside and outside the house, and caulk all gaps or places that air could infiltrate.