>  However, we appear to lose that change (the pixel, and the TrueColor

Try the same experiment with a PNG image.  JPEG is a lossy format so
it may lose the change in the one pixel you made.  Also try with
ImageMagick 6.3.1.  If that fails, post a small script that illustrates
the problem.   If we can reproduce the problem, we will have a fix for
you within a few days.
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