Playback Errors

There seems to be a bug in MS4 where when I load in a .mscx file (originally made in MS2 or 3) some notes will be randomly (significantly) quieter or simply will not play at all. When I click the note it will play. When I check the properties the velocity is standard, and the "play" box is checked. When I play from that particular note, the note will play but start later than other instruments (or i.e. later with respcect to the metronome). When I start the playback from before the note in question, playback will skip the note entirely.