So, here's the deal. It doesn't matter what I'm doing. I could be surfing the web, or reading emails, or even doing c4d work and all of a sudden, I get a thunderstorm sound that sounds identical to a certain game I spend too much of my life on (Minecraft). I check. Have I left Minecraft open? Nope. Have I left my window open, and it's storming outside? Not a drip. I proceed to close all programs running. Still going. The next thing I do is I open up minecraft to see if it's raining in any of my worlds. It is in one world. /toggledownfall. Still, I get this raining sound.
One thing I do pick up on is that when I go into the Services and Processes window ( I do that with a third party program ), I see that Java is running. So, I close it. The rain stops.

The bottom line? Java seems to be screwing with me, and not dropping the audio files when the game stops.