Have you considered using some of the timers as counters? When a processor is overclocked it reaches a point where parts inside start to fail at the clock speed for whatever reason, such as internal rise time. This normally does not damage the part but since it is not working properly the results are not correct either. There are a lot of other things that happen as well but this I believe may be your problem. Also be sure it is not operating to hot, as you speed it up the temperature range it will operate in diminishes.
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