Trying to diagnose noise in speakers

I have an old 5.1 surround setup. The speakers sat in storage for probably a year before hooking them back up. Now, I have an occasional noise that comes through. When my machines turns off in power saving mode, the subwoofer will do a faint "wub" every half second or so until it kicks back on. The noise isn't constant and varies by what I'm actually doing. It actually gets bad during gaming but even then it seems to vary by title. Starcraft 2 is horrendous. Bioshock Infinite is fine. But for other uses like youtube, hulu, netflix it's fine and is faint enough to be drowned out easily by the normal sound of what's playing unless you turn them down really, really low.

I use on board audio so I tried plugging in some headphones into the front jack on my tower. The noise was still there too in one instance of it being particularly bad. So, I'd like to figure which is exactly wrong. When the noise is low, sounds come through crystal clear still and the subwoofer still has kick so I'd rather not replace them if possible. How do I isolate the cause?

Thanks.
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More about diagnose noise speakers
  1. try to disable the line in recording device. that used to do the trick in the old win xp. not sure where that is now on win 7/8
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