The most common cause of thumping noises in wind is a damper in a ventilation duct. If there is ventilation duct from cooking equipment, bath or dryer that exhausts at or near the roof, the wind can open and close the damper (flapper) causing noise. The solution may be as easy as applying a piece of tape to cushion the damper blade as it closes. This may be located in the eaves or through the roof. As an experiment, next time you hear the noise, go around and switch on any exhaust fans you might have. If the noise stops, you found the problem.