Did this work?
I had the same exact problem (MZNH900)... and I did not have Synch mode enabled - at least it's "off" now and I don't recall ever changing it. Online Sony service told me to send it in for repair, though I didn't think to mention that I was using the optical input. Also, I would get track markers in the middle of music. Worse, when I recombined the tracks, there were repeated segments. Are there any other possibilities?