I made all test.
I am quite sure it is 5V powered up.
When the motherboard is powered but off, first pin of the power button header is nothing (not grounded) and the second is +5V.
If I short to ground the first pin, the second or both, nothing happened. But if I supply +5V to first pin, the motherboard wake up.
My shut down controller do not short pin together, it shorts pins to ground. But ground, this is not +5V so the motherboard do not wake up.