I've been having the same issue and it seems to only take affect at higher altitudes and only from my left set of speakers (5.1). I have onboard audio on an Asus M4A89GTD PRO.
When I get up to altitude it will start to make the crunching/crackling noise from left speakers with distorted audio only from those speakers and then cleans itself up after 10-20 seconds.
Unlike you I have only had this issue since upgrading to Beta 3. The last time I had it happen after leaving the game none of my audio seemed to work besides teamspeak 3. Running the 32-bit executable in Windows 7 64-bit.