Sounds like the troubleshooting I just had to do. I'd suggest checking pin 14 of the COP. That pin is ~3v when the system is off, 0.5v when the system is on, and 5v when the power state is changing (powering on or off). This pin is supplied power by 1K resistor R46 form the 5v standby rail, and is pulled low by pin 39 on the keyboard 6552 pin 39. If the 6552 had failed it could be holding that pin low, making the COP think the system is already powered up.
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