I noticed the multiple thread thing and chose to ignore it....simply because I thought it would derail focus. And it did. Got a big run-on sentence and half my questions unanswered. However, just enough info to set Synthjoe onto:
My guess is that your sample clock runs at a very low frequency, but I have no idea why... Who's the sync master? Maybe the BNC cable is broken? Maybe the desk is set to 32 kHz (but I think it runs even lower, maybe something around 4 kHz)?
...which I think is the most likely culprit, given the nature of the distortion. Brian, you really need to concentrate on the details of things...otherwise we all wind up playing 20 questions trying to pull answers out of the air.
For instance, I noticed you mention a patchbay. How is that incorporated into your setup? When you say no patchbay" what exactly did you do to eliminate it from the equation?
You also mention that you've been hearing this distortion from tracking all the way through mixing. That only means one thing to me: something that is common to both units. Synthjoe's guess of clocking issues is a good one. Another common thing to both is any analog interface between the two....like badly grounded patchbays, incorrect "normalling" and mix n match of balanced and unbalanced connections. I still want to know how you generated that test file....from cradle to grave.
Another thing is to ask the most fundamental and classic beta test question: If everything worked and then stopped working as expected....what changed? You're really going to have to put some thought into that answer.
Meantime, start checking the integrity of your WC cable between the D8B and HDR and all the WC settings that are available in both units. That's a good start.