Your comment confuses me. I installed the "HN Toolkit", but it doesn't "show 5 new items at bottom of main page"; it shows the last 30 new links to the right of the normal homepage content.
Anyway, you might want to try installing again. I updated the script to play nicely. (I didn't test any of the other features that the Toolkit provides, however.)
http://userscripts.org/scripts/show/25039