Today I am facing the same problem, with a slightly different environment. I used Emacs 24.3.1 on Windows 7, and then switched to the same version as Cygwin + XWin with the same .emacs.d configuration. Although the clipboard on Windows worked fine, with the configuration I had under Cygwin / XWin, I had the same problem as in the question.
In the terminal, it worked fine, and XWin -Q also worked, so after a little digging it turned out:
;; MS Windows clipboard is UTF-16LE (set-clipboard-coding-system 'utf-16le-dos)
I don’t remember why I added this. I must have copied it from some Emacs Wiki in the early days. When I googled now, it looks like a popular setting in people's configurations. It turns out that under Windows I do not need this line for the clipboard to work correctly with Emacs (quick check with some concise diacritical characters), and under Cygwin / XWin it finally started working.
source share