Interestingly, I picked up a 4Pre a few days ago and am having random, intermittent noise on the Thunderbolt buss myself on my late 2013 iMac. Mails to Focusrite have been met with silence for three days so far, and I've done a LOT of troubleshooting myself.
I've reset SMC, PRAM, tested hardware from OS bootup, uninstalled Focusrite drivers and tried it that way, reinstalled the drivers, disabled journaling, played with sample rates, disabled wireless ethernet and bluetooth, tried different Thunderbolt ports on the machine, tried different power outlets both using a Furman strip as well as a plain wall outlet, unplugged studio monitors and XLR's from the interface to eliminate outside noise entering, even tried the interface on my Macbook Air to isolate the iMac from the equation... Everything was met with the same issue, random noise upon recording and playback at random points in the timeline. The noise also changes the tonality of an instrument so it's very evident that it's occurring.
My particular iMac is not one that is affected by the issue described on the Focusrite page, I have a totally different model year, however I can't be sure as I have no way of testing the Thunderbolt buss/cable itself.
I can at this point only conclude that the interface itself is causing this, some form of noise leaking into the Thunderbolt buss or a fault in the drivers used that is causing some digital noise in the chain, something of that nature. My old Tascam US-1800 USB2 never had issues like this up until it's demise at which point this was to be it's replacement. Now I'm left with two interfaces that are unsuitable for production, lol.
I'll update this post in case we reach a resolution, hopefully this information will help someone else as it seems that there is little to no information on this specific issue. I like the interface, but if this is what I'll be met with using Thunderbolt, forget it. I'll go back to USB interfaces without these glaring issues.