Let me see if I can help you.
First off don't worry about damaging your pedal set. It is very robust, just watch the wires and remember where everything goes back together.
Turn your pedal set upside down. There is a small black set screw, either 2mm or 2.5mm, on the shaft that goes to the silver box ( sensor ) . Remove the set screw ( nothing will happen ) and get a flashlight and look into the hole. There should be a shallow hole for the set screw to go into. If you don't see the hole then the shaft is not indexed correctly with the magnet on the end of the shaft to the sensor.
To correct this problem you have to remove the 3 allen screws holding the sensor on ( watch out for the 3 nylon spacers because they are easy to lose ). Push the shaft partially out from the non magnetic end about half way to expose the set screw hole you would looking for. Turn it with your fingers to line both holes up and the push it back in. Be patient trying to push it back in ! Take the flashlight again and make sure the 2 holes line up. Once they do, put the set screw back in and do not over tighten.
Replace the sensor and the nylon spacers and again do not over tighten.
Since you said you have done nothing to the pedal set I guess it is possible for the shaft to come from the factory misalligned. If in fact this is the case you will get the symptoms you are having. If the 2 holes line up and you still have the problem, Fanatec will be your answer.
Good luck,
John