Its in a funny place. you actually have to look at the compressors page and they have a link to the factory paperwork that comes with the compressor.
http://www.rparts.com/Catalog/Major_Components/compressors/Danfoss/BD50F_compressor.pdf
When I built my little home brew unit I used a standard Thermostat that is just wired into the speed circuit. Set the speed at a medium level. Pretty simple.
The compressor speed is controlled by how much resistance is in the circuit completing it. Reading about some piggy back controllers like the Temptech
http://www.great-water.com/pages/Temptech/Temp_tech.htm The default would be to freeze if it can't regulate the temp. If it is the Danfoos controller then the speed circuit would have to be damaged and I suppose reverse polarity could do that.
Both boards being replaced is kind of freaky that you still have the problem. The core compressor is just a DC motor. If it can cool then I seriously doubt its the problem. It would not cool if it was damaged. All the controls of it are on the power leads to the motor.
When you replaced the controller did you also replace the temp probe? A fridge temp probe would be the only other thing I could think of that would cause this if replacing the other boards didn't cure it. Put a ohm meter on the leads to the probe and fire it up and make sure you are getting a change in resistance as the box cools.