I ran into a similar problem a while back. My three week old gigabyte cooler would only spin 2500, whether it was set at 4500 or not. I unplugged it and re-plugged it in a couple of times, just checking things, when I turned it back on, it was running normal.
What cooler do you have? Does it have a controller or temp sensor for the fan?
My Desktop: <A HREF="http://Mr5oh.tripod.com/pc.html" target="_new">http://Mr5oh.tripod.com/pc.html</A>