Motherboard power-up issue
I find the question appropriate and well formulated - then again, I myself am a noob around here.
Parakmi has clearly found the block diagram in a Winbond datasheet, here is a copy:

and he comments on the individual signals quite correctly.
My own knowledge does not go far enough to give you a statistic of typical causes, but from my perspective of a PC repair techie this kind of a problem means that the motherboard gets shipped to the mobo maker's own repair center, where often one of the large chips (here probably the south bridge) gets replaced. Which involves BGA package soldering and requires that you have a spare chip in the first place. Vendors of industrial motherboards do this - e.g. Advantech still can and does repair motherboards for Pentium 4 processors. Noone does that for ancient office-grade PC hardware.
= before you scrap the motherboard, maybe try replacing its 3Volt battery (often a CR2032 coin cell) - the power sequencing blocks inside the south bridge (and the SuperIO chip) depend on that battery-supplied rail, and can make the board misbehave in mysterious ways if the battery is half-way dead.