timidity -Ow is not running in realtime, so a low-latency kernel will not make a difference. There is actually little sense in that noise: either something in your processing chain is expecting raw input and misinterpreting the wav header, or your sound fonts have problems: try installing and configuring a different set (I think there are several). However, the music sounds as if it were having identical repeats (does it?) in which case it would make little sense if the noise occured only at the start.
So all in all, I can't really produce a sensible interpretation of your described results. Maybe the description is missing something, and maybe my ideas will help you figuring out something. I do seem to remember that I had similar noise problems with some music and changing the sound fonts (to "freepats" or the other way round) cured it.