I read through the posts that discussed this issue and the solution was to use the "[BUGFIX 3.4.1/3.4.2/3.4.4] Getting Configure Excerpts to work in all cases."
Since I have the newest version of Atahualpa (22.214.171.124) installed that fix has already been applied. Yet, I still have the problem where the last word in my manual excerpt does not show up for each post.
I can add a random word to the end and it will then add that last word I want but I was hoping there was a real fix somewhere.
I also have Wordpress 2.9.1 installed