I'll second the observation that hot machines flake in odd ways. It's not just the processor- hot memory is also unpredictable- hard drive controllers- "northbridge"- you name it- there are many essential parts that can overheat and cause you hard-to-diagnose grief.
If cooling your machine doesn't work, could be a power supply issue, they seem to die before the rest of the computer and sometimes do so slowly. Low power also causes erratic behavior.
