Since Ashkenazim and Sephardim/Hasidim put on tefillin differently from each other, it might be important to know your particular tefillin minhag.
The fact is, Ashkenazim wrap the strap of the shel yad inwards (towards themselves), and so naturally both the yud kesher and the loop that the retzuah goes through is towards the body.
Sephardim and Hasidim, however, wrap the strap outwards (away from themselves), so the yud kesher will be on the inside on their arm, but the loop that the retzuah goes through will be on the outside of their arm. (Does that make sense?)
Take a look at this webpage from R' Melech Michael's, a reliable sofer, showing pictures of different tefillin minhagim in order to help someone determine their tefillin minhag. You will notice that the second and third picture look very similar, even though the second one is of left-handed Ashkenazi tefillin and the third one is of right-handed Hasidic tefillin.
Perhaps your rabbi is not familiar with the minhag of the Sephardim/Hasidim, ie, wrapping outwards, or he did not look at your tefillin in great detail. The second explanation makes much more sense, as a rabbi should know this minor difference.