Recently I had a failure building mingw-w64-x86_64-emacs-git on MSYS2 and flagged it to Emacs people,
http://lists.gnu.org/archive/html/emacs-devel/2016-03/msg00130.html
A short discussion,
http://lists.gnu.org/archive/html/emacs-devel/2016-03/msg00143.html
http://lists.gnu.org/archive/html/emacs-devel/2016-03/msg00157.html
was cocluded with this fix,
http://git.savannah.gnu.org/cgit/emacs.git/commit/?id=69e03ddccf47fc29126317dd3317313ecd92b797
I wonder if you have better ideas..
See also
http://lists.gnu.org/archive/html/emacs-devel/2016-03/msg00162.html
http://lists.gnu.org/archive/html/emacs-devel/2016-03/msg00164.html
etc..