Case fan continously Speed up then down

[fonzie]

I recently upgraded to a Supermicro X9DR3-LN4F+ along with 2 E52690 V2 chips. I kept my same case and fans which are as follows Norco 4224 with noctua pwm fans. The issue that i keep having is that my fan speed will go from low to hight evey couple of minutes. I have monitored my temps and they seem to be fine. The only issue i see is that my motherboard is warning me about fan speeds. My current fan speeds range from 2100, 900, 525 but all temperatures are in the low side. The motherboard shows from warning to critical and the one thing that i have noticed is that if I set optimal speed it will set them back to full speed. Not sure if this is due to the warnings that it changes the fan speeds to speed up and slow down. Any help would be appreciated.