Boot up your computer with the sidepanel off of the case. Listen and look which fans are causing the problem - the CPU fan, which case fans, etc.
cscgal
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Why don't you check out download.com for those programs that gamers and overclockers use to measure fan rotation and CPU temperature? Oh wait, that won't work - it only happens at bootup, right? :-/
When this happens, do you notice the computer feeling any hotter than usual? I can't really offer much more advice given there's no way to find out *which* fan is the problem - cpu or not.
A similar thing happened on my mac when there were some low level hdd errors. I would turn it on and the fan would just keep getting louder and louder and the computer would never boot into OS X. I reformatted and the problem instantly went away.
cscgal
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When I boot one of my systems, the following happens once in a while. One time it just loads nicely without any noise, and the second it loads like a fan is running at full power, once the system is fully loaded the noise has reduced.
What you are describing is a common problem with cheap sleeve-bearing DC brushless fans. As the lubricant dries out with age, it becomes gummy and sticky in the bearing. This also throws the blade off-axis. As the fan warms up due to friction from spinning against the gunk, some of the gunky oil melts and acts like it's supposed to, lubricating the bearing and allowing the shaft to re-center.
When you get the unit open (I don't think you have much of a choice), you can use the "poor man's stethoscope" -- an old paper-towel tube -- to isolate the noisy fan. Sometimes (rarely) they can be lubricated, but replacement is best.
In a case like this (in both senses of the word) I would use aPanasonic brand fan, as they are the best quality available, by far. I get them from Digi-Key .
TallCool1
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