Hi Doug G,
I think the bios just sets up the initial hardware config for the nic as the mainboard needs to be able to supply power to the pci bus whilst the pc is off. The nic also has to be able to use the supply of power to keep the network link live and to be able to trigger the psu through the mainboard on receipt of a magic packet (the actual wol function). So I don't think it matters which state the PC is in (suspend, hibernate or fully off) when it does receive the packet.
I think my current issue is that the OS is disabling the on-nic wol function but the bios is still providing it power (which the nic is not using due to that wol function now being disabled).
I have never had this issue before with any OS either, even though the option in the OS to change the nic wol function has been available, I have never used them as I have always relied on the bios power to pci setting.
This is what has thrown me in this case as I don't seem to be able to find the case of it being disabled on every reboot.
Sorry about the waffle, I am explaining it to myself more than anything and don't mean to sound patronising :o