I might be missing your point, but I repeated the steps I mentioned in Ubuntu and have success. No middle click pasting though, just the OS X/Windows/everyone else standard of either context menu pasting or Ctrl+V. I recorded it too: http://www.youtube.com/watch?v=nZl3gTzqyKA
For unix systems with X, you copy the text by selecting it. So when you want to paste a URL, selecting the old URL to delete it will overwrite the copied URL. You would need to delete it first, and then copy the URL you are after.
Again, though, I think I'm missing something. Isn't the windowing system Ubuntu uses X? In my video demo I "select" the contents of the text box, yet the existing contents of the clipboard remains. Or is this something Ubuntu does to keep us "other platform" migrators happy?
There is another clipboard that X users like using and don't like having obliterated whenever a program requires text selection. The ctrl-C/V clipboard and the highlight/middle-click clipboards are different.
This won't work when using the primary selection (ie. middle-click paste) in X. Selecting the text wipes out the previous selection.