I fully agree with the pilot light cleaning idea. If that doesn't offer any help, you might want to adjust (or cause to have adjusted) the pilot burner pressure. There is an adjustment for this purpose on the main gas valve. It might need a little more pressure to have a decent enought flame to overcome the occasional gusts of wind down the stove pipe. The data plate of the water heater lists the proper pilot burner pressure in inches of water column ( "wc).
"Nothing is foolproof to a sufficiently talented fool"