I'm not clear on why the sound changes. Is it just better when you have music playin or something. There may be another problem if the noise changes that drastically. I'm not sure if this has anything to do with it, but does the noise get worse when you've had it on for a while and heated the water up, or is it just noisy sometimes when you start it up, and not other times. Best bet would be to see if just resting the pump on a sock or something and closing the case to see what the best noise might be if you stop it from rattling. Wouldn't leave it there because it's not secure but you'd see the difference of rattling. If the pump still has variations in the noise I'm not sure what might be causing it. I have some thoughts but i'm still in the process of making my own watercooling aparatus to test stuff with. BTW what case are you using for your system?