Found the answer to two different errors that were causing the topics to get out of sync and get "sick" as it was put, in my upgraded forum.
1) When I upgraded I had a user from Denmark using a different language prior to the upgrade. He clicked to Watch this Topic, but when a reply was posted it attempted to find the old language file for the e-mail template, but since English is the only language file present it failed. I went to edit his profile and English is now in the database as his language, and the problem went away.
2) Another topic got "sick" and out of sync. Again, someone had chosen to watch the topic, but their e-mail address as in the database is wrong, so the send mail failed. When I stopped then from watching the topic the thread was once again back to normal. I sent them a PM and asked them to update their e-mail address.
I hope that this will help others to solve their problems related to posts gettting out of sync.