xindy.pl incorrect bin path? Or incorrect invocation?

Dear MiKTeX users,

I am transitioning over to xindy from makeindex and was running into
problems where makeglossaries.exe gave errors due to xindy.pl not being
able to find the bin path.  Looking into xindy.pl at the line number given
(415, in this case), I saw this relevant line:

elsif ( -d "$cmd_dir/../../miktex/bin/x64/internal" ) {    # MiKTeX 64-bit
       $cmd_dir = "$cmd_dir/../../miktex/bin/x64/internal";

(I am on 64-bit MiKTeX, obviously)

I printed out the value $cmd_dir to debug the issue and it gives me:
C:\Users\MYUSERNAME\AppData\Roaming\MiKTeX\2.9\scripts\xindy

This path is where the Perl script is run from, but *not* where
makeglossaries.exe is run from (which invokes xindy.pl).  Therefore, when
it tries to go backwards two directories (../../) from $cmd_dir, it is
looking within my user AppData stuff rather than the MiKTeX installation
which is in C:\Program Files\MiKTeX 2.9\miktex\bin\x64.

I am able to have everything working properly by changing xindy.pl and
hardcoding the MiKTeX bin path.  But, I think this is not what is supposed
to be happening.  I installed everything via MiKTeX's package installer -
nothing manual.  So, I am wondering if the configuration (e.g. xindy.pl
location or xindy.pl's path determination) is wrong?  Or am calling
makeglossaries.exe incorrectly (using "@makeglossaries.exe -d _build_files
"%1"" from the base path of the .tex file I am working with)?

I added the xindy.pl path into TeXworks, just to be safe, but the same
behavior occurs.  Also, searched around for details and configuration, but
most of the xindy stuff relating to MiKTeX that I found is ~1.5-2 years old
or seemingly irrelevant to this issue.

If anyone knows what is going on, that would be great  If I can present any
additional details to clarify, let me know.  Thanks in advance!

Best,
Chris
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