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What would stop a CRTDUPOBJ of a logical from pointing to the physical
file at the top of my library list?

I don't think CRTDUPOBJ uses the library list.

I created my duplicate physical file in my test library, using CRTDUPOBJ
(with data *yes).
I added the test library to the top of by library list.
I created my duplicate logical file in my test library, using CRTDUPOBJ
When I perform a dspfd, the new logical is still pointing to the original
physical.

This is from the help (F1 key) for the CRTDUPOBJ command:

    When a logical file is copied into another library, two cases
    determine the basing for the file:

      1.  If both the logical file and its based-on physical file are
          originally in the same library, a duplicate of the physical
          file must be created in the new library before a duplicate of
          the logical file is created.  After these two duplicates are
          created, the new logical file is based on the new physical
          file.

      2.  If the logical file and its based-on physical file are
          originally in different libraries, it is not necessary to
          duplicate the physical file before duplicating the logical
          file.  In this case, the duplicated logical file is based on
          the same physical file as was the original logical file.
          Unlike the first case, even if the physical file is copied
          into the new library before the logical file is copied, the
          duplicated logical file is based on the original physical
          file, not on the duplicated physical file.


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