Not manually, no. The temperature sensors for inlet are on the front panel, so they are probably not detecting the overheating on the hard drives.
Which chassis are you using? Is it a pedestal with an 92mm fan behind the hard drive cage?
I'm using the Intel® Server Chassis SC5650DP that has fan the behind the HDD cage, so where are the sensors placed ?
The temperature sensors for inlet are on the front panel. I don't think that backplane monitors hard drive temperature, though.
You could always try chagning some settings in the fan control menu in BIOS (change altitude, quiet to performance mode, etc.) to see what effect it has...