I have found a temporary solution. I am using a Saffire Pro 40 and it is doing the same thing with QuickTime videos. I use Google Chrome, so I am not having issues due to video. I am also not having issues with sound in FInal Cut Pro X or Logic Pro X.
Right click the quicktime video and "open with" iTunes. iTunes will play it instead of quicktime. When I do that, it no longer has the click and pops.
Of course some of you are saying you are getting the click and pops on iTunes. I do not. Only on Quicktime.
Another thing, QuickTime does not do the click and pops when I use the speakers to my Macbook pro or Thunderbolt display. Only when I use the Saffire pro 40 through my studio monitors. Hopefully they fix it soon, especially if I run into something bigger than just having to play QuickTime video's in iTunes.
As far as you who have big libraries of stuff that is not working. I would not convert those librarys to anything else right now. Just wait and see what happens. And try to play it iTunes instead of Quicktime and see if it works.