I was just looking at 5v 3v3 Level Shifting Experiments and wonder if the Pi Droid Alpha Servo pin level shifting resister divider method affects the HC-S04 echo timing or accuracy?
When I had the echo going direct to the GPIO w/o the proper level shift, the distance readings seemed quite close to the mm. I did not re-check after I rewired the echo to go through the servo block (level shift protected).