Zotac has been very proactive with getting me updates on its motherboard, I have their excellent North American PR rep to thank for that
As I mentioned in the last update, the Zotac Ion board won’t wake up from a S3 sleep state after activity on a USB device (e.g. moving your mouse, hitting a button on a media center remote, etc...). Zotac listed the problem as being a hardware issue that won’t get fixed until the next revision of the motherboard; early adopters are out of luck. I now have an explanation as to why.
The USB ports on the current version of the motherboard (PCB version 00) are powered by the 5V rail from the motherboard. When the motherboard goes into a S3 sleep state, 5V power is shut off, so the USB ports are completely off.
In the next revision of the motherboard (PCB version 01) standby power will be connected to the USB ports, allowing the ports to still be alive when the board is in S3. The manual shows you where you can identify what PCB revision you have.
I’m guessing externally powered USB hubs are able to pull the system out of sleep since the USB device is still on, but a USB device connected directly to the motherboard will be completely powerless in S3. The explanation makes sense to me; if you were wondering, now you know.