I have encountered this sound corruption as wlel with my new TBD. I run a MBP Retnia tied to 2 Promise Pegassus Raid arrays. I took the monitor in for Apple to check and of course they were unable to reproduce the issue. I started nosing aound the net an came upon Anandtechs TBD review.
http://www.anandtech.com/show/4832/the-apple-thunderbolt-display-review/10
On that page listed, it seems Anand reveals the source of this issue (at least in my case). It stems from high I/O read and write of the Pegassus drives. In fact the issue most likely is with the Pegassus drives firmware.
I'm going to pick up my TBD from apple and will bring it up to the Apple tech. And I will also call Promise, to see what they know of the issue.
So do any of you also have a Promise Pegassus raid in your setup?