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I'm not real sure what your problem may be but the heatsink will get pretty warm but you should be able to hold your finger to it without getting burned. Make sure the heatsink is put on properly and is sitting down flush on the processor. What processor and Heatsink/fan are you using? Sounds like it may be a slot type with two fans. You need to be sure the fan you used to replace the bad one is moving enough air too, it could be too small in volume of air for the one it is replacing.
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