This is probably due to the fact that certain parameters in Emacs are terminal-specific, and the manipulation of such settings in the initialization file affects only the terminal that is active during the evaluation of the initialization file.
Q + A :
/ Emacs
, , :
(defun my-terminal-config (&optional frame)
"Establish settings for the current terminal."
(if (not frame) ;; The initial call.
(xterm-mouse-mode 1)
;; Otherwise called via after-make-frame-functions.
(if xterm-mouse-mode
;; Re-initialise the mode in case of a new terminal.
(xterm-mouse-mode 1))))
;; Evaluate both now (for non-daemon emacs) and upon frame creation
;; (for new terminals via emacsclient).
(my-terminal-config)
(add-hook 'after-make-frame-functions 'my-terminal-config)