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Try runing a hardare monitoring program and log the temp. and voltages. I had a computer awhile back where the +12V line dropped to ~10.5V whenever it was under full load. I ended up having to replace the mobo. If it starts happening more frequently it's worth looking into.
For a quick test try hooking up a multimeter to one of the molex connectors and run doom 3. Watch what happens when it restarts.
If the fan doesn't have an rpm connector it's not going to register as running.
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"Empirically observed covariation is a necessary but not sufficient condition for causality" - Edward Tufte
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