First, have you updated to X3b? This sounds like the same type of issue in X2 with moving MIDI notes with the mouse. Any movement, whether large or small, would cause CPU spikes and scratchy sounds to the audio/playback stream. I think it's a Windows vs. Mouse vs. Sonar issue. I say this because I've noticed scratchy audio while using applications other than Sonar when, for example, iTunes is playing in the background. And overall, my computer is very good with audio streaming, i.e. it has low latencies for normal operation (checked using dpclat.exe).
Can you try moving clips and notes around to see if this also happens in your projects? If so, then the issue still remains in X3. Also, while doing so, and while moving your knobs on your VST's, run dpclat.exe in the background to see if you get spikes. Thanks!