the singular form of evidence is not anecdote. I think it's an interesting conundrum myself. as others have pointed out, the story as it was told is not consistent with the physics and current knowledge of what things were like in those days: CPUs did not yet do thermal throttling and simply cooling a CPU from that time doesn't make it go faster.

somebody else mentioned the possibility that the cooling did something to the crystal oscillator, but I think there are another two explanations that either alone or in combination might explain what happened: unreliable narrator (OP was very young when the memory was formed) and external influence - his dad or teacher might have done the overclocking which might have been beyond his understanding and therefore notice at the time.

either way there's no reason to take anecdotes uncritically.