@samlogan87 the auto tune function attempts to tune for fastest response. To achieve lower noise, you probably need to use lower R values than the auto tune function suggests. As you are now using 30 and 40, try 15 or 10.

The forthcoming 3.5.0-beta.3 release allows you to specify a velocity feedforward term in the M569.1 command. That may also hep to reduce noise.

I will revisit the noise level of closed loop motors later this month/early next month.