I have 24.3. And I cannot reproduce the problem with this version.
There gud-display-line
looks as follows:
(defun gud-display-line (true-file line)
(let* ((last-nonmenu-event t) ; Prevent use of dialog box for questions.
(buffer
(with-current-buffer gud-comint-buffer
(gud-find-file true-file)))
(window (and buffer
(or (get-buffer-window buffer)
(display-buffer buffer))))
(pos))
(when buffer
(with-current-buffer buffer
(unless (or (verify-visited-file-modtime buffer) gud-keep-buffer)
(if (yes-or-no-p
(format "File %s changed on disk. Reread from disk? "
(buffer-name)))
(revert-buffer t t)
(setq gud-keep-buffer t)))
(save-restriction
(widen)
(goto-char (point-min))
(forward-line (1- line))
(setq pos (point))
(or gud-overlay-arrow-position
(setq gud-overlay-arrow-position (make-marker)))
(set-marker gud-overlay-arrow-position (point) (current-buffer))
;; If they turned on hl-line, move the hl-line highlight to
;; the arrow's line.
(when (featurep 'hl-line)
(cond
(global-hl-line-mode
(global-hl-line-highlight))
((and hl-line-mode hl-line-sticky-flag)
(hl-line-highlight)))))
(cond ((or (< pos (point-min)) (> pos (point-max)))
(widen)
(goto-char pos))))
(when window
(set-window-point window gud-overlay-arrow-position)
(if (eq gud-minor-mode 'gdbmi)
(setq gdb-source-window window))))))
The window
setting is completely different from yours. Maybe, the above code is helpful or maybe you should upgrade to the new gud/gdb stuff.