I've noticed that after I deploy my Help system and then conduct a search that the words on my "always ignore" and "stop" lists are still appearing when I search them (such as "a" and "the"). Are there any extra steps to deploying the stop list that I am missing?
Are those words in your stop list? Always Ignore is index related rather than search related.
Test in a new project to see what happens there.
Also create a copy of your project and then reset the Stop list to see if that changes things.
See www.grainge.org for RoboHelp and Authoring tips