Just in case anyone's using Wavosaur for any of this analysis - when I was testing RMAA, I noticed that THD increase by 300% after I did something with Wavosaur. So I did some more testing and found that simply opening the RMAA file and re-saving it increases RMAA's THD measurement by 300%. I tested with Adobe Audition and it didn't have this problem. Using Audacity, the THD increased by 100%. I assume/hope it's dithering causing this.
EDIT: In CEP I just trimmed my reference to 1.486 secs and trimmed a recording to the same length. Then I did the Invert/Add of the two files, ran a 64K fft and the difference file now shows levels of about -120db worst case and average on both channels of -146db , this is broadly in line with earlier attempts. Different window types do show sligthly different results but thay are all very close.
One final test: Digital silence of 1.486 and a low level -72db white noise add the two together = > white noise at -72db (diff test - all 000.000000)
And now for the bad news...
I took two recorded samples trimmed to 1.486 (65536 samples) did and invert/add and the difference file was averaging -144db with a peak at -115db. Tried this with a couple of different pairs getting similar results , thus the inter-sample variations are bigger than the differences between any 1 sample and the reference, thus it will be necessary to do many trials and average the results before any possibility of useful comparisons, but it does not bode well, now an average of -144db is small potatoes in real money but if differences do exist between optical cables in pure data transmission terms, they would have to be pretty sizeable to overcome this.