Does the New Reputation line only display if you have a new reputation comment?
I used to have this add-on and the New Posts and Reputation count add-on installed. I had the New posts one installed so that I could get the New Reputation count. I had the manual edits to the navbar template. When I saw that the new version of this add-on added in that ability, I removed the New Post and Reputation count-add on. My manual edits are still in there. I removed them from one of my styles, and when I refreshed my forum, there is no New Reputation line as in the screenshot you posted.
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