Ok, I changed our test set-up to more closely match your configuration. I connected two H9000s with S/PDIF over RCA where one was the clock master and the other was the clock slave and was receiving clock over the S/PDIF connection. Both H9000s were running at 96K of course. I didn't hear any audible distortion or clicking in this configuration.
To Nick's point, the cables we have connected are relatively short and they are cables that were manufactured with the correct impedance for S/PDIF. Not to say that your cables don't match these specs though of course; your cables might be perfectly fine…
