Audible noise coming from Inductor when using LT3760 driver circuit
Here is the standard circuit provided by LT: -



I note that your circuit does not have 5x 2.2 uF capacitors on the output of your boost regulator (after the schottky diode, D43). I've drawn a red circle around them.

This could easily be a significant factor in causing your problem. It's there to smooth the current through the inductor when the LEDs are being switched with PWM. Try it out.

If they are present and you haven't shown it on the diagram then you are naughty.