Linux has – for historical reasons – two clipboards. One is the one that old X hands will know and love, the other is the new one. And the two are completely separate. If you put text in the copy-buffer (the X windows style clipboard), then you attempt to paste out into a new-style application, nothing will happen. Likewise the other way around, copy out of an application that uses the new style clipboard and the X applications won’t know there’s any text in the clipboard. Because there isn’t.
So. How to get around this problem? On debian/ubuntu, there’s a package (which isn’t installed by default) available to install. autocutsel. It’s a background application which knows about both styles of clipboard and attaches to both. When one changes, it’ll synchronise the two clipboards.
Downside? If you’re used to two clipboards and know which applications use which clipboard (and you exploit this mercilessly) then you’re going to lose the contents of the “other” clipboard with this running. Enough of a bummer to stop me using it? Nope. It’s a beautiful little application which allows me to copy and paste between all my applications – including those pesky mono applications. Yay!