Mac Mini Mid-2012 Fan Noise

I replaced the hard disks in my Mac Mini Server Mid-2012, and replaced the 1x500GB with 2x256GB SSD. They aren't the Apple model - they are Samsung.

Ever since then, the fan runs at maximum speed, regardless of ambient temperature. This is the Mid-2012 model so there aren't separate temperature sensors. I've replaced the fan, and get the same issue. I'm now running Sierra, but the problem happened before the upgrade to Sierra.

I've tried installing smcFanControl and used the command line functionality to set a maximum fan speed, or a constant fan speed, and the Mac Mini seems to ignore it.

If I read the temperature sensors on the hard disks, it's clear that they aren't working correctly: the readings come up as blank.

Any advice on how to solve this would be much appreciated.