Actually some systems, such as AMD XP platforms, and VIA C3 systems, power the CPU from the 5v rail.

It's really hard to say what went wrong. Perhaps there is some internal trouble with the PSU. If that were the case though, I would expect you would have seen similar symptoms in the 4 pin molex connectors. They should have overheated as well. I would pin it on either Mobo or CPU.

Let me know what the platform is, I might have a compatible mainboard kicking around in the basement that is not in use. I have at least a dozen. AXP, PIV, PIII, etc.