EMS Battery Backup

Your interpretation of the pin orientation for X3 is correct.  Take a look at the wiring diagrams in section 24-00-00 of the Rotax 912iS install manual.  Diagram 3:15 is a good place to start.  The start power switch and the battery backup power switch work much the same.  Each will connect the airframe ground to the regulator A ground bus (which is normally isolated).  However, the start power switch supplies +24v to X3 pin 2, whereas the battery backup power switch supplies +24v to X3 pin 1.  With the master switch and battery backup power switch on, and the start power switch off, you should have +24v at X3 pin 1 in reference to the ground bus on regulator A.  Is it possible your mechanic did not have the Master Switch on in addition to the Battery Backup Switch?