This behaviour has always been the case and is a design feature of X11.
You are describing SELECTION and PRIMARY buffers. They were separate and have semantics that are both supported by major X applications. It is unlikely that this will change in the near future, even though more and more applications prefer exposing the PRIMARY buffer in their menu systems."
Ubuntu QA guy Simon Law puts it like this:
"Thank you for your report.
This behaviour has always been the case and is a design feature of X11.
You are describing SELECTION and PRIMARY buffers. They were separate and have semantics that are both supported by major X applications. It is unlikely that this will change in the near future, even though more and more applications prefer exposing the PRIMARY buffer in their menu systems."