The site-specific pieces of the initial load-path are different in the
nt/msysconfig.sh build from how they used to be with nt/configure.bat.

In src/epaths.h (when built), PATH_SITELOADSEARCH is defined as:

  with nt/configure.bat: "%emacs_dir%/site-lisp;%emacs_dir%/../site-lisp"

  with nt/msysconfig.sh:
"%emacs_dir%/share/emacs/24.3.50/site-lisp;%emacs_dir%/share/emacs/site-lisp"

The former version was much more useful on Windows, allowing
one to keep a bunch of Emacs installs in a single parent directory
that also contains the site-lisp directory.

As a workaround I tried configuring with
"--enable-locallisppath=c:/emacs/site-lisp" but it didn't seem to have
any effect.

In GNU Emacs 24.3.50.1 (i686-pc-mingw32)
 of 2013-05-30 on 57172UHB
Bzr revision: 112785 xfq.free@gmail.com-20130530092755-xhnwfx1wk3ueebnk
Windowing system distributor `Microsoft Corp.', version 6.1.7601
Configured using:
 `configure --prefix c:/emacs/emacs-112785
 --enable-locallisppath=c:/emacs/site-lisp CPPFLAGS='-I G:/usr/include'
 LDFLAGS='-L G:/usr/lib''

Important settings:
  value of $LANG: ENG
  locale-coding-system: cp1252
  default enable-multibyte-characters: t

Major mode: Lisp Interaction

Minor modes in effect:
  tooltip-mode: t
  mouse-wheel-mode: t
  tool-bar-mode: t
  menu-bar-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  line-number-mode: t
  transient-mark-mode: t

Recent input:
M-x f i n d - l i b <return> s i t e - s t a r t <return>
M-x r - e - b <return>

Recent messages:
For information about GNU Emacs and the GNU system, type C-h C-a.
find-library-name: Can't find library site-start

Load-path shadows:
None found.

Features:
(shadow sort nadvice gnus-util mail-extr emacsbug message format-spec
rfc822 mml easymenu mml-sec mm-decode mm-bodies mm-encode mail-parse
rfc2231 mailabbrev gmm-utils mailheader sendmail rfc2047 rfc2045
ietf-drums mm-util mail-prsvr mail-utils thingatpt find-func time-date
tooltip ediff-hook vc-hooks lisp-float-type mwheel dos-w32 ls-lisp
w32-common-fns disp-table w32-win w32-vars tool-bar dnd fontset image
regexp-opt fringe tabulated-list newcomment lisp-mode register page
menu-bar rfn-eshadow timer select scroll-bar mouse jit-lock font-lock
syntax facemenu font-core frame cham georgian utf-8-lang misc-lang
vietnamese tibetan thai tai-viet lao korean japanese hebrew greek
romanian slovak czech european ethiopic indian cyrillic chinese
case-table epa-hook jka-cmpr-hook help simple abbrev minibuffer loaddefs
button faces cus-face macroexp files text-properties overlay sha1 md5
base64 format env code-pages mule custom widget hashtable-print-readable
backquote make-network-process w32notify w32 multi-tty emacs)