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auxiliary fan going crazy on windows boot-up

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Hey guys well heres my story.

when i got my PC around 3-4 years back it was a stock PC from a computer retail store. pentium 4, 150g HDD. none of its specs were anything fancy. Now back then this problem started, my auxiliary fan at the back panel of my PC would start spinning at like 90-100% speed. At first i was pretty surprised but after about 2-3 minutes it would go back to normal. this occured on and off with like 1 or so weeks between events and eventually going away.

Then 1 and a half years ago i stripped out everything in my PC. motherboard, cpu, gfx card. everything except the case and cd drive. Back then i had a similar problem but it was my second gfx cards (i have 2 gfx cards in crossfire) fan this time. that was easy to take care of because i could just tell it to shut up using "ATI overdrive" (the gfx cards own driver software).

But now my auxiliary fans started going crazy again and now its worse. Everyday on boot-up atleast once it will go insane and will not stop. i do have a sort of cheap solution which is to let windows fully load and then do a standard shut-down, wait like a minute then start-up again.

What i need help with is if anyone could give me a solution on how to tell my fan to slow down without me actually disconnecting it. i know i dont NEED the aux fan but my room gets really dusty and i dont want a massive hole in the back panel of my PC. plus my PCs cooling isnt exactly high tech so the fan kind of helps (but its enough to know that my PC isnt super spinning the fan because its overheating).

Any help appreciated.
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    Grumpy Ol' MSgt (Ret.)

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Where is the fan connected too, the motherboard, or directly to the power supply? If the power supply, it should run constantly at full speed. If the motherboard, then depending on the motherboard, it should speed up and slow down as temperatures rise and fall.

You can buy a new fan with a speed controller, or buy an in-line speed controller, and connect directly to the PSU. Then toggle down the speed so it is not so loud. But of course, be aware that slower speeds mean less cooling so you need to watch your temps.

Also note that dust creates a very effective blanket, trapping heat. So I recommend you inspect the interior monthly, and clean when necessary.
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