Update
I have tried all the usual suspects to resolve it. I have switched to the backup bios and it does it there as well, so F7 or F8 version of the bios does it. I have removed all cables from the back of the PC and it does it, so no peripheral are causing this. I have switched all the Wake on Lan setting both on the bios and in Windows. I have also checked the power leads from the case power button to the motherboard and that is fine as well. The only thing I have not tried is another power supply. This power supply came out of another computer and it was working fine in that PC, so I assume that its still good and should not be doing this in this PC.
Anyone have any suggestions on what else I could try?