Is it a weird kind of background type noise? Kinda kard to notice unless you're paying attention? I had a similar thing, where my computer made a high-pitched noise when I was running RC5. I'd pause the client, the sound would go away. I'd start it again, and the noise would start. It also did weird things, like the noise would stop for a second when those help-type 'what's this' popups come up in windows and stuff.
It turned out that my motherboard was dying 🙁 One day my computer just died, and wouldn't post anymore, so when I opened it up, sure enough there was this black smudge on the motherboard where one of those donut-shaped-copper-wrapped thingies used to be (to use the technical term).
So, um, that's probably not what you wanted to hear, but that's what ended up being the problem with my computer 🙂