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Make sure that you have the latest BIOS.
Do a CMOS clear on the board.
Once this is done, note down the cpu temperature and the cpu fan speed from the bios.
In the BIOS, there is a section for fan control.
Go to Advanced
Go to Fan Control
Try to change the settings and see if it makes any difference.
And try to install the new Intel Desktop Utilities (even though it is not meant to be used on old board - it worked fine sometimes)
Try to check the cpu fan speed from the monitoring software as well.
Let me know how it goes.
Thanks for the suggestions. However I have tried all of these solutions. The BIOS is the latest version. I cleared it out with the jumper. There is NO section in BIOS setup which lists temp or fan RPMs. Desktop utilities was no go as well. I did get the fans down by cheating though. I wired them both into the 5V side of a molex connecter and plugged them directly to the PSU. Nice and quiet now. And I didn't notice any drastic spike in temperature. The funny thing is that this board didn't seem to care that the CPU fan was unplugged from the motherboard. No beeps, error messages, classical music or anything. Maybe there's something else wrong with it.
I am sad that you could not find where the problem is exactly. When you unplugged the cpu fan, it wont issue any beep, the only thing that will happen is the cpu temperature will invrease gradually.
If the cpu load is at its maximum, eventually the system will shut down automatically. Probably, it is worth of changing the cpu fan for a high profile fan.
I remember that cpu fan spins at its maximum when it is plugged on a chassis fan header. It is not advisable to do that.
Now regarding the Hardware Monitoring, so I remember that there is an option in the BIOS.
Advanced >> Hardware Monitoring
See Picture Below:
If you have temperature higher than 75C or CPU fan running at full speed, then it can be due to any of these:
a) bad integration
b) PSU not ATXv2.2 for recent board
c) Chassis is not TAC (Thermally Advantage Chassis)
d) Bios Issues
May be you can test the system out of the chassis and with another power supply V2.0 at least.
Other than this, I cannot see any other things that I can advise you.
I guess I missed this when you replied 2 years ago. Sorry. I just want to clear up one thing. I did not leave the CPU fan off. That would be unbelieveably dumb. What I meant was that I wired it directly to the power supply on the 5V rail. I was just surprised That I received no "fan out of range" messages.
Thanks for everyone's help on this.