Unlikely, there are a few reasons why. First of all the threads are drawn from the data in the threads views table, which is the same for ALL forum members, no personal profile settings could/would have an affect on that. The very same code is also used to determine the next/prev links on the message view pages, which is why I was surprised by your report that next/prev links are correct.
If you have a threaded view enabled, could you check & see if the dupe message appears on that view as well?
As well as check the 'thread_view' MySQL table for any duplicate entries by running the a query such as this:
SELECT thread_id,pos FROM {PREFIX}thread_view WHERE forum_id={FORUM_ID};