How come I got different results when I take the same measurements on the same pairs of images multiple times? 

Answer:

If variation in measurements is small, the most likely cause is that you may not locate the corner points exactly the same from one run to the next. If variation in measurements is large, the most likely cause is that you may not locate the reference in the images accurately or the reference used is too small comparing to the size of the objects that you want to measure. In this case, it is necessary to choose a larger (longer) reference, obtain its true dimension accurately, and measure its locations carefully in images.

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