It's not temperature but "working" warning. Though, I'm pretty sure you meant that.
I had the same problem after installing an aftermarket cooler. Turned this warning off - a shame really as it would be good to know when the CPU fan fails.
Frankly, I don't get why this problem is even there. I mean, shouldn't the MB know that it's due to it's own tampering with the fan speed?
As it is, I can't use this warning at all as my CPU fan runs at 200-300 RPM when I'm not doing anything load-heavy.