I'm in a very similar position as you farquea, with 100 new H61M-P23 boards installed. I've spent over an hour trying to fix this, trying every possible permutation of relevant settings without success, updating the BIOS, changing power settings to OS controlled rather than BIOS, and setting the OS settings to wol on magic packets and wake from shutdown, disabled EUP2013. Nothing's worked. It won't even WOL from S3. It won't even USB device wake from S3. The whole power control thing seems to be FUBAR in fact. Avoid this entire range of MSI boards if WOL is important to you.