Bob van der Poel, Jun 30 2016:
...

(well, a bit more complex since the file is a midi and it's played via
timidity).

I find that the start of every song presents some distortion for about a
second. I'm assuming that it has to do with the audio port being opened or
initialized.

Hey hey Bob,
I just made sure and tested it with Timidity here. No such distortion. My Timidity uses JACK as its default output. Could it be your playback arrangement? I remember having similar issues with a pair of dynamic headphones, which could adjust incoming volume. If the incoming material was too loud, after a bit of silence, it would distort for a second.

Have you checked the issue with other sound sources? Some multimedia player? Or have you connected another playback device than your laptop to your amp? -- Granted perhaps stupid questions, but sometimes odd things do happen.
...

Ta-ta,