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I'm sorry if this comes out blurry - I'm tired.
I wouldn't rule out a software error, but it doesn't sound like it because of it's irregularity (of course, from what you're saying).
A relatively far fetched problem would be the CPU, unless it's relatively new and should automatically slow down in case of overheating. If it's older and, e.g. the thermal paste between the heatsink/fan and CPU permits air pockets that could lead to overheating and crash. Low conductivity would explain higher rpms - on the other hand the fans on some systems do start high automatically and then wind down fast. Either way, and I'm rambling, doesn't sound like that kind of problem. CPUs don't half die or half crash, thus not creating these sorts of issues.
Bad ram - if possible (available on Linux (on boot), perhaps live cds too, don't know about win), run memtest86 to check for faulty memory. This sounds most likely and is not too uncommon.
You have not so far hinted on anything that points towards the harddrive.
PS. Overclocking can lead to overheating and the overall higher operating temperature of components to a shorter life span. DS.
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