P.S. Here is my init.el


(setq load-path (cons "~/.xemacs/tnt-2.6" (cons "~/.emacs.d" (cons "~/.emacs.d/tsgates-git-emacs-799d9a8" load-path))))



(custom-set-variables
  ;; custom-set-variables was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 '(comint-input-ring-file-name "(concat \"d:/My Documents/.history/\" (format-time-string \"%Y%m%d\") \".hist\")")
 '(cygwin-mount-cygwin-bin-directory "d:/cygwin/bin")
 '(desktop-save-mode t)
 '(ediff-cmp-program "d:/cygwin/usr/bin/cmp")
 '(ediff-custom-diff-program "")
 '(ediff-diff-program "d:/cygwin/usr/bin/diff")
 '(explicit-shell-file-name "d:\\cygwin\\bin\\bash.exe")
 '(gitk-program "/usr/bin/gitk")
 '(tramp-default-method "scp")
 '(tramp-encoding-command-switch "-c")
 '(tramp-encoding-shell "d:/cygwin/usr/bin/bash.exe"))
(custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 )


;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Initial setup
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; This assumes that Cygwin is installed in C:\cygwin (the
;; default) and that C:\cygwin\bin is not already in your
;; Windows Path (it generally should not be).

(setq exec-path (cons "D:/cygwin/bin" exec-path))
(setenv "PATH" (concat "D:\\cygwin\\bin;" (getenv "PATH")))

;;   LOGNAME and USER are expected in many Emacs packages
;;   Check these environment variables.

(if (and (null (getenv "USER"))
	 ;; Windows includes variable USERNAME, which is copied to
	 ;; LOGNAME and USER respectively.
	 (getenv "USERNAME"))
    (setenv "USER" (getenv "USERNAME")))

(if (and (getenv "LOGNAME")
	 ;;  Bash shell defines only LOGNAME
	 (null (getenv "USER")))
    (setenv "USER" (getenv "LOGNAME")))

(if (and (getenv "USER")
	 (null (getenv "LOGNAME")))
    (setenv "LOGNAME" (getenv "USER")))

;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; (A) M-x shell: This change M-x shell permanently
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Would call Windows command interpreter. Change it.

(setq shell-file-name "bash")
(setenv "SHELL" shell-file-name)
(setq explicit-shell-file-name shell-file-name)

;; Remove C-m (^M) characters that appear in output

(add-hook 'comint-output-filter-functions
	  'comint-strip-ctrl-m)

;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; (B) *OR* call following function with M-x my-bash
;; The M-x shell would continue to run standard Windows shell
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(defun my-bash (&optional buffer)
  "Run Cygwin Bash shell in optional BUFFER; default *shell-bash*."
  (autoload 'comint-check-proc "comint")
  (interactive
   (let ((name "*shell-bash*"))
     (if current-prefix-arg
	 (setq name (read-string
		     (format "Cygwin shell buffer (default %s): " name)
		     (not 'initial-input)
		     (not 'history)
		     name)))
     (list name)))
  (or buffer
      (setq buffer "*shell-bash*"))
  (if (comint-check-proc buffer)
      (pop-to-buffer buffer)
    (let* ((shell-file-name            "bash")
	   (explicit-shell-file-name   shell-file-name)
	   (explicit-sh-args           '("--login" "-i"))
	   (explicit-bash-args         explicit-sh-args)
	   (w32-quote-process-args     ?\"));; Use Cygwin quoting rules.
      (shell buffer)
      ;;  By default Emacs sends "\r\n", but bash wants plain "\n"
      (set-buffer-process-coding-system 'undecided-dos 'undecided-unix)
      ;; With TAB completion, add slash path separator, none to filenames
      (make-local-variable 'comint-completion-addsuffix)
      (setq comint-completion-addsuffix '("/" . ""))
      ;;  This variable is local to buffer
      (setq comint-prompt-regexp "^[ \n\t]*[$] ?"))))

;(defun my-shell-setup ()
;;   "For Cygwin bash under Emacs 20"
;;   (setq comint-scroll-show-maximum-output 'this)
;;   (make-variable-buffer-local 'comint-completion-addsuffix))
;; (setq comint-completion-addsuffix t)
;; ;; (setq comint-process-echoes t) ;; reported that this is no longer needed
;; (setq comint-eol-on-send t)
;; (setq w32-quote-process-args ?\")
;; (setenv "PID" nil)
;; (setq shell-mode-hook 'my-shell-setup)

(require 'cygwin-mount)
(cygwin-mount-activate)

;; Already loaded in Emacs23
;; (load "~/.xemacs/nxml-mode-20041004/rng-auto.el")

;; This seems to screw me up. Besides, it looks old.
;; (load "~/.xemacs/nxhtml-2.08-100425/nxhtml/autostart.el")

;; Could this be the culprit?
(load "~/.emacs.d/xquery-mode.el")

(server-start)
(put 'narrow-to-region 'disabled nil)