When my gas water heater fires up, there's sometimes a flash of flame at the vent opening where the vent pipe attaches and a sharp whop sound.
I suppose what's happening is that the gas turns on but doesn't ignite right away; by the time ingition happens, there's gas built up. (Just like a gas stove will do.) Maybe it's a pilot light problem or a dirty burner?
It's a GE model SG40T12TXK00 - a 40 gal, Ultra Low-NOx unit, less than a year old. I think this just started to happen.
I keep the intake vents clean, so I don't think that's the cause.