i have this problem as well.
sometimes using winAMP to play back anything -- flac, mp3, raw wav -- results in a playback that's about as great as a weak AM signal!
but sometimes... it's as clean as if i were using one of my other media applications.
it's not a winAMP eq curve issue. (i'm on v2.91, btw. if there's a newer version for which flac/shn plugins work, let me know!)
i've thought in the past that it's codec related, because i remember the problem occuring for the first time just after i installed the divx codec.
oh yeah, that's another thing -- playback wasn't always this noisy. for the first few weeks after i built this system (nforce 2 chipset, AMD 2800+ barton proc) i was fully content, but then after installing x,y and z applications/codecs/etc, voila, i noticed this hissy playback.
i've always had on the back burner to wipe the drive, reinstall OS and test playback after each install in the hopes i could narrow it down, but... that rainy day has not yet come.
if anyone has any advice on this problem, i'm all ears