I have actually been experiencing the same with Studio 9...
It happens when I import mpg footage. Symptoms are no adio in editing untill I play each clip through a little then the adiou comes in and seems okay. Run through all the clips, doing the same to each clip & then everything's fine in the preview. Burn to VCD & the audio is either non-existant or sporradic...
I've not had any probs with avi footage though