I don't think that it's ML related - may have something to do with your TB port - have you tried using both on your rMBP? With the same results?
I hate to say it, but you may have to bundle the whole kit up and take it to your local Apple Store or an AASP and see if it's a display or rMBP TB problem. I don't have a rMBP - just a regular old late 2011 15" - and the sound is quite good through the ATD speakers.
I have the exact same issue. I hauled the TB Display into the Apple Store 3 times and finally they replaced it. Come to find out this new one has the same issue still. So It has to be rMBP related at this point. Unfortunately I don't think I have it under warranty still and the issue is hard to demonstrate. I recorded videos of it but every time I go into the store and plug it is the same as switching the speakers from internal to external and it takes 30-60 mins before it degrates to scratching sounds.
Please let me know if you ever foudn a solution. Im going to try to keep taking it in until I can get this resolved.