This always seems to happen with integrated sound. The problem is that it's difficult to properly isolate the sound "card" circuitry from the rest of the motherboard; therefore, the analog pre-amp picks up noise from all the signals coursing through the MB, amplifies the noise, and outputs it to the speakers or headphones.
I have an Asus P4P800-Deluxe which outputs noise during IDE activity, but only through the analog speaker/headphone output. I use the digital audio output, which turns out to be noise-free, to connect to my HT receiver, so that's my work-around.
If your MB supports digital output, you can try a speaker set that supports digital input (or a receiver/speaker combo that supports the same--like many inexpensive new HTIB setups I've seen), a new seperate sound card (might not be an option though, depending where you work), or just live with it if it's not too loud (turn off your speakers unless you're listening to something). Unfortunately, there's probably no free fix.