You need to follow a process of elimination. I've been using MIDI since before there was MIDI and I've never had a problem with skipping notes. Try the following and post your answers:
Are you using a real synth or a softsynth? If a real synth, check your cables and interface.
If a softsynth, is it particular to one softsynth?
If you change the track to a different softsynth or a different patch, are the notes skipped?
Are the notes skipped always the same notes or different?
Load Tutorial1.cwp, assign the tracks to the TTS-1. Do you get any skipped notes?
You should be able to figure it out based on these tests.