I had the same problem until recently running SCP in Windows XP, intermittent crackling and popping sounds at random intervals. Turns out my drivers for the on-board Realtek soundcard were the culprits, even though it worked fine in every other game I own.
If you have on-board sound by Realtek, I'd check to see if there's a newer driver version to try. This might be totally unrelated since it's a different OS, but your description fit my symptoms perfectly. Can't hurt to check I suppose.