It happens with anything with audio. the demos in the iDemo, games, midi file playback, mp3 playback, etc.
There is less crackling if running at stock speed but still far from perfect. It is really bad when running WinUAE at fastest speed which pimiga requires. Perhaps I should try building my own hardrive image with workbench. I don't particularly like Pimiga anyway as it's too flashy for someone who only remembers the A500 with WB1.3
I only tried the Pimiga image for a quick and dirty test.