What BIOS version are you using? According to Intel, the latest BIOS for the DH55HC is "0028 12/1/2009" link
Did you have this problem before updating tthe bios?
If your CPU fan is not running the cpu will be damaged.
My bad. I was using that one. Its the only one I've ever had. Actually, my CPU temp is about 29 degrees C, and the fan is now running, but it is still not being detected and the BIOS is still detecting the input fan as the out take fan.
You could try clearing the CMOS or back flashing to the previous revision of the BIOS. The latest revision is not too recent so hopefully they will release a new rev. soon.