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Congratulations on building an outstanding system! MSB makes very high quality gear! It sounds like a possible compatibility issue - which doesn’t surprise me when dealing with the very temperamental technology of Clocks. That said, unless the Aurender MC10 is bringing a performance level that you can just cannot be without - you may want to consider replacing it.
There are many Digital Cable choices out there offering both BNC and AES/EBU connections. This is such a challenging area due to the unpredictable sonic results any given cable can have with different systems. For this reason, I srongly suggest visiting www.usedcable.com and picking out a number of cables that can be shipped to you for audition with the allowance of returning the ones you did not like. This gives you the ability to have some fun swapping out those cables and arriving at the right choice.

