Q: Weird noise from audio interface when using Thunderbolt port

Try a NVRAM/PRAM reset:

http://support.apple.com/kb/HT1379

Also check applications/utilities/Audio MIDI set up and make sure the settings are correct for your set up 44100.

This is strange, not heard of this before.

You can try a SMC reset, don't know if it will help, but it can't hurt anything.

http://support.apple.com/kb/HT3964

Since you say it recently started, I wonder if the interface has developed an issue, if possible see if you can borrow a different one to check that.

Yeah, no surprise about the smc, but a benign thing to try.

I would try to get my hands on another usb interface and see if that particular unit is not happy with the Mac. Also try changing out cables one at a time to see if there is a cable that is not 100%, doing them one at a time may help isolate the issue.

This kind of thing kinda sounds more hardware related than a software thing. Since you say that recently it started would tend to point towards something has possibly gone into some failure/near failure mode.

I'm having a similar problem while using this setup: "Focusrite Clarett 4pre" thunderbolt audio interface and an early 2011 Macbook Pro

Focusrite has been amazing at trying to figure out what the problem is, but I have a feeling it's our laptop model. That early 2011 Macbook pro edition seems to have so many problems with it.