If you look at the source code
(defun window-configuration-to-register (register &optional arg) ... (set-register register (list (current-window-configuration) (point-marker))))
you will see that it saves the point as the second argument. Just reformulate it as
(defun my-window-configuration-to-register (register &optional arg) (interactive "cWindow configuration to register: \nP") (set-register register (list (current-window-configuration) nil)))
and override the Cx rw shortcut and also use my-window-configuration-to-register
(define-key (current-global-map) (kbd "Cx rw") 'my-window-configuration-to-register)
Or define advice
(defadvice window-configuration-to-register (after window-configuration-to-register-no-point activate) "Avoid storing current buffer position in the register. We want to stay on the last used position, not to jump to the saved one" (set-register register (list (current-window-configuration) nil)))
The only problem is that when you click on it, an error message appears. You can override jump-to-register to avoid this.
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