When I attach the microphones the accuracy falls off to plus minus 10K cycles.
You have to think on the measurement approach (and physics) when getting such results. How is the measurement setup? Are you sure you measure only the wave's front hitting mic1 and then mic2 and in that precise sequence? There could be a lot of sound waves mixing, bouncing around.. When the mic1 is close the mic2 the mic1 may deform the front shape of the wave, etc.
http://www.acoustics.salford.ac.uk/schools/teacher/lesson3/flash/whiteboardcomplete.swf
