When you select an item to paste, that item should advance to the top of the list.
E.g. You have a list of 20 items in clipboard history, you select the third item (counting from top) from the list. The item is pasted (or not, depending on your setting), and also is shown as the first item (counting from top).
This 'feature' should be available as a hidden setting. In the terminal you should paste the following command to enable it:
$ defaults write net.sf.Jumpcut pasteAdvances 1
and the following to disable it:
$ defaults write net.sf.Jumpcut pasteAdvances 0