Please explain the hole in the roof thing.
FVIR water heaters are susceptible to lack of adequate combustion air. This is not related to the flue, which must be proper for any gas appliance. Where is your WH located? In the garage, or in a closet?
Have a plumber check the maintenance manual for your water heater. It may be the type which needs to have the lint screens cleaned inside every year.
Could you post a picture of your exhause flue pipe set up?? I don't like the sound of what you describe/