It is close to twenty years that I have been using GNU Emacs almost daily, and you still figure out new stuff.
I’ve been somewhat annoyed that copying and pasting between Emacs and Gnome applications were so inconsistent, and then its all in the manual:
Using the Clipboard
As well as the primary and secondary selection types, X supports a “clipboard” selection type which is used by some applications, particularly under OpenWindows and Gnome.
The command `M-x menu-bar-enable-clipboard’ makes the `Cut’, `Paste’ and `Copy’ menu items, as well as the keys of the same names, all use the clipboard.
You can customize the option `x-select-enable-clipboard’ to make the Emacs yank functions consult the clipboard before the primary selection, and to make the kill functions to store in the clipboard as well as the primary selection. Otherwise they do not access the clipboard at all. Using the clipboard is the default on MS-Windows, unlike most systems.
Maybe its time to read it again.