X has two "clipboards": the primary selection, and the clipboard. Emacs 23 uses the primary selection by default, but it seems you want the clipboard. You can enable this with the following in your .emacs
:
(setq x-select-enable-clipboard t)
This setting changed in Emacs 24 to use the clipboard by default. See also: http://emacswiki.org/emacs/CopyAndPaste