Well I used to hear them too on my MacBook air running Linux.
Now Linux Mini is 20.1, Pulse Audio is 1:13.99.1, and Squeak is 6.0alpha with update 20211, and the VM is from sources of 202101092147.
And the Bach fugue sound perfect.
So something changed to make it work well.
Does a recent VM plus a recent Squeak 6.0 Alpha make the PI sound good?
Thanks.
bruce