During startup, Emacs initializes itself according to a given code/file order. If some of the code executed in your .emacs file needs to be postponed until the initial terminal or window-system setup code has been executed but is not, then you will experience this problem (this code/file execution order is not enforced after startup).
To postpone the execution of Emacs Lisp code until after
terminal or window-system setup, treat the code as a lambda
list and set the value of either the
term-setup-hook or window-setup-hook
variable to this lambda function. For example,
(add-hook 'term-setup-hook
(lambda ()
(when (string-match "\\`vt220" (or (getenv "TERM") ""))
;; Make vt220's "Do" key behave like M-x:
(global-set-key [do] 'execute-extended-command))))
For information on what Emacs does every time it is started, see the lisp/startup.el file.