Causes of the choppiness could be a lack of resources like processing power or RAM. Or it could just be a bad chipset driver, try downloading all the newest drivers for your motherboard if you're using onboard sound.
Causes of the crackling could be a bad driver or just the on board sound picking up the movement of the head on the hard drive. I get this all the time but can't hear it over the music. It's actually why I purchased a sound card for my home desktop, I was getting the feedback from Audacious (Linux Winamp).
Or it could all be caused by Windows Service Pack 3, there's a method for removing it on the internet, you don't need it in your car. In fact I think all service packs are pointless if the computer's not hooked up to the internet. The method involves a very long string entry but I know it works.