I use Sonar 6 too and I have had plenty of issues like this. Sometimes on a certain beat, it won't play any VST synths. Even if I solo the track and just bounce that one, the note is still missing. I've also encountered sampling issues with Battery 3, where Sonar cuts the sample short - especially noticeable with a cymbal hit. Luckily in that instance, just closing and reopening Battery fixed the problem.
One thing I have noticed in both the synth and sampler issues is that the dropped notes vary depending where your start your piece. Do you have these problems during playback or just when you bounce? I experience problems with both- any dropped notes heard during playback will also be dropped in the exported wav.
I just chalk it up to glitches, I imagine Sonar 8 doesn't have these problems. One of these days I'll have enough money.....