i use a clipboard manager (parcellite in 10.04) and it works just fine, text is available even after program it was copied from gets closed.
if you want to check what's in the buffers, install xsel
$ xsel --help
-o, --output Write the selection to standard output
-p, --primary Operate on the PRIMARY selection (default)
-s, --secondary Operate on the SECONDARY selection
-b, --clipboard Operate on the CLIPBOARD selection
primary is used with highlight-copy/middleclick-paste, clipboard with ctrl+c/ctrl+v