I've been working with MIDI for over 20 years and this has been driving me crazy for the last hour. I've never had it happen before.
I've opened up, in SONAR, a MIDI file that I created in Band In A Box. Push play and it sounds fine using my computer's built in Microsoft GS Wavetable Synth.
To get a better quality sound, I insert an instance of Cakewalk TTS-1 and point the tracks to it--a separate channel for each track--and I'm hearing about half of the notes. It more or less randomly (?) just doesn't play some of the notes on a busy picked guitar track. It doesn't play any wrong notes--just doesn't play some of them. (Looking at Piano Roll View, there might be an issue with identical notes being played at the same time--except one of the guitar picking tracks is on Channel 3 and the other on Channel 6. Polyphony and choking shouldn't be an issue, right?)
I've gotta be missing something simple here and just suffering from temporary insanity (which might become permanent if I don't get this figured out).