Had the same problem 20 years ago.

After I installed a between-the-studs thermostatically controlled
exhaust fan in my unfinished attic to remove some of the sweltering heat
build-up, I experienced the negative pressure situation others have
alluded to. I could smell the water heater flue gases being drawn into
the house because the exhaust fan was sucking outside air down the
chimney. Nasty.

To remedy the problem, I installed an interface between the water heater
and the exhaust fan, that would shut the fan down while the water heater
was doing its thing.

I purchased a Fenwal Thermoswitch with specs appropriate to the
temperature range I would be adjusting it for, then punched a hole in
the flue pipe to accomodate insertion of the sensing tube into the flue.

The Thermoswitch is line voltage capable, but would have required
running BX cable from the water heater to the attic, so I opted to use a
low voltage wire run instead, utilizing a relay to handle switching of
the line voltage.

When the gas fired water heater kicks in, the Thermoswitch senses the
hot flue gas, and shuts the attic fan down. When the water heating is
done, the flue cools off, and the attic fan comes back on.

Here's a pic of the device installed atop the water heater:

http://d21c.com/krnspn/MISC/TOOLS/wa...ermoswitch.jpg

Joe