Clipboard persistence is a bug that affects many programs under Ubuntu and other X11-based operating systems. Fixing it is a Google Summer of Code 2010 project.
The problem: data loss on quit
If you copy something from an affected application and then close it, you'll have an empty clipboard.
Workaround: Clipboard Managers
If you want to fix this problem on your machine, you can install a clipboard manager that should solve it. I recommend Parcellite.