I found what's going on by running the command manually:
src/bootstrap-emacs.exe -batch -l "/C/Users/Haroogan/Projects/GitHub/MINGW-packages/mingw-w64-emacs/src/emacs/admin/unidata/uvs.el" --eval '(uvs-print-table-ivd "/C/Users/Haroogan/Projects/GitHub/MINGW-packages/mingw-w64-emacs/src/emacs/admin/unidata/IVD_Sequences.txt" "Adobe-Japan1")' > /C/Users/Haroogan/Projects/GitHub/MINGW-packages/mingw-w64-emacs/src/emacs/src/macuvs.h
Loading macroexp.elc...
Opening input file: no such file or directory, c:/C/Users/Haroogan/Projects/GitHub/MINGW-packages/mingw-w64-emacs/src/emacs/admin/unidata/IVD_Sequences.txt
The path gets messed up somehow.