Flame adjustment and control

I have an Aero gun mounted on a New Yorker oil burner. I recently had smoke coming out of the burner. Took apart and vacuumed out the entire burner (lots of soot) and changed nozzle. The fire box is cracked in several places so a new burner is on the horizon. Put back together and adjusted air so I i have a nice bright yellow flame. Obviously, you don't want a dark yellow flame as this will promote soot build up. My question, when running the flame has the appropriate bright yellow flame but when the burner shuts down the flame goes to dark yellow color for two seconds or so before shutting down?