Well, I dont have a quick fix for your problem, or any idea why you get it. But, I can suggest that you consider getting an optical amp to connect to your SP1300 (which i do believe has optical outs from the M/B). If you read this List Of 5.1/optical Amps
post you can see that some of the people posting note that they get no noise at all when using an all optical system.
So, with a 250-500 dollar investment you can not only get rid of the thump, but most likely all noise coming from the computer. (I Think).