Hi , I got a similar situation.
Everything (audio and synths) plays fine until I do a bounce-to-clip. After this all the synths start to sound distorded/fragmented. The audio clips (not the synths) continue to play well (undistorted).
The problem disappear if I (save the project) and I restart it, restarting the whole program Sonar X2 (but I had the problem also with Sonar X1).
I tried the suggestion I read in this forum, incresing the latency ... without restarting the program ... and effectively (if I increase it alot) the problem disappear.
Anyway it is not logic to solve such problem increasing the latency because, as said, it works fine (with the smallest latency) until I don't do any "bounce to clip".
So it is the "bounce to clip" action that "brokes something".
The problem should be solved by the developers I guess (I am a computer developer too)
NOTE : effectively my project is a big project with many synths and a long track 18+ minutes