Well, I've experienced this and to me it was all about discovering a new thing about Sonar and MIDI.
It may not be the case but give it a go.
Right click on a MIDI note that doesn't make any sound. There should be a box saying "Channel" and this might say something entirely different than "1". If it does, then this is most likely why you don't hear any sound when it triggers. When you record MIDI, the MIDI chanel on your controler is apparently inserted into the note data and will playback that particular note on channel 2 - or whatever it's set to. Some VSTs will play back that note on a different channel than what the loaded instrument is geting it's input from. This way you can load one patch for kick and snare (channel 1). one patch for hats and toms (channel 2) and the last one for cymbals (channel 3) in Kontakt for example, and just use one MIDI track to control the three different channels. However, I believe this doesn't apply to Session Drummer so it just play back all the MIDI that is sent to it. I think it's a bit of old school MIDI. IDK.
so check the silent notes to see that they are sending to channel one (or whatever channel the notes you
can hear) and you should be able to play back all the notes.
You can highlight all the silent notes and change the channel in the Event Inspector if I recall correctly.
I hope this helps.