IIRC, you tuned the PID coefficients without the fan, then turned the fan on during the print. Autotune sets the control coefficients for best heat control under the conditions it sees, so you must do the tuning with the fans running if that's how you'll be printing.BBID wrote:short of running autotune again
Although better tuning may get you closer to the goal, remember you can see surface finish effects you cannot measure. Simple things like a vertically repeating infill pattern (changing the spacing of the perimeter thread), periodic filament diameter variations (due to control loop hunting on their extruder!), a slightly eccentric drive gear (tiny speed variations every 38 mm of filament), or a flaw on the filament spool ID (snagging slightly on each revolution) can produce barely visible changes in the extruded thread.
You're fighting the process, which generally ends in heartache & confusion …