I have the same issue - I changed the motherboard (had a Gigabyte ATX and moved the old gear into a Zotac mini-ITX) and immediately noticed the low frequency drone associated with any any video update. I'm using the IGP via DVI output. Note that only the MB, RAM and case changed so I'm pretty certain the audio circuit on the motherboard is not well layed out resulting in interference from the video lines. I'm thinking about putting a high-pass filter between the speaker output on the MB and my speaker plug since it sounds like hum is < 100 Hz. Really annoying since I put this thing together to be a HTPC...
I hate to say it but I can't recommend the Zotac M/B because of this even though it had a great feature set (supported fast AM2 desktop CPU i.e. could recycle the old PC, high memory capacity etc in mini ITX, but the sound issue is a show stopper.
Edited by hamluis, 10 September 2010 - 11:04 AM.
Split from similar topic ~ Hamluis.