I'll explain what voicegroups are, first. When you listen to the song when it's still a .mid file, your computer will play that song using a set of 128 preinstalled instruments (if you have a sound card). However, after converting the .mid into a .s file and assembling it into Sappy, it will be assigned to a voicegroup, which is like that set of 128 preinstalled instruments. But due to the way the devs of the Pokémon games set up the voicegroups, each voicegroup only uses around 10 instruments (rather than 128), which means that all tracks of your midi, which use an instrument that is excluded in the voicegroup you assigned your .s file to while assembling it, will sound like a mess of electric noises.
What game are you using? To the left of the volume slider in Sappy, you'll see something that reads "Voices 0x[pointer]" What is the offset for that pointer?