Very interesting Steve, I saw the same problem with just a gravity feed meths burner also. It is in a vertical boiler with fire tubes. I only use it occasionally to run a stationary steam engine. Will try a blower next time.
Steve When the burner is mounted in the boiler firebox the flames are still strong and steady for about five minutes. Then the flames become unsteady and start to pulse. That is, the flames will alternatively die back and then flare up before dying back again.