I used to have this extremely infrequently. Now, with 3.5, I get it so often that it basically ruins the whole experience for me. I even get random crackles in game too. Something is really wrong with this update.
Go on the official forums and report it because Valve isn’t going to look here for bugs.
I have this problem. The audio crackling is especially bad and even setting the GPU speed does nothing to get rid of it. Often times I will launch New Vegas and it will crackle. I will have to relaunch it positive several times to get it to launch without crackling severely. Even still, I have had several games (New Vegas, Persona 3 Portable, Knights of the Old Republic II, Sonic Adventure 2, Mass Effect Legendary Edition, etc) crackle while playing them for a short while and this is a new development with 3.5; I didn’t have this with the previous stable OS 3.4.