Okay, this is a little confusing (and more annoying!)

Reason:
When you install Windows, it takes the power setting that's in the BIOS and never changes. So if you have S1 set in the BIOS, install Windows, and then set it to S3, Windows will always revert to S1 for standby regardless of the BIOS setting.

*sighs heavily*

So...

Simple solution:
Set your motherboard to S3, and re-install Windows.

Not-so-simple solution:
There is a utility called dumppo.exe, hidden in the darkest corner of Microsoft.com that could help you. Here's a link to it.

What this is is it's an administrative override for the Windows suspend settings. I can't find any detailed information on it, and I can't test it myself. So from here on in I'm afraid that I'm completely guessing.

I think that this utility will permenantly set Windows suspend to S3. First of all, run it under cmd.exe with these parameters:

Code:
dumppo admin /?
This list displays the current sleep states for your computer.

To override the maxsleep state, use one or other of the following parameters:

Code:
dumppo admin /ac maxsleep=S3
Code:
dumppo admin maxsleep=S3
Dumpo.exe doesn't have to go anywhere: you can run it from the desktop. I think the latter command just puts the computer in an S3 standby state, whereas the former does the actual override.

Anyway, that's all that I can help you with. You're probably going to have to fiddle around with it yourself. Good luck man.


By the way:
Description of how to enable the S3 system power state for standby when USB devices are armed for wake