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.