yeah its annoying, but in Music 2000 it happens even if the sample offset is at 0. It mostly happens if the note fade in/out is set so there are no fade in and notes are stuck together. Listen to my Final Fantasy 6 trance remix for an example (listen carefully to the song bass)
There isn't much way around this, except to alternate between two channels for every notes in a riff. like put note 1, 3,5,7,9,etc in channel 1 and 2,4,6,8,10 in channel 2. THis also prevent notes from cutting each others.