Okay, well the long and the short of it is that after running install.php my "Forgotten Towns" category shows up twice. I know it shouldn't, but it does. Full stop, there's no arguing that it has happened.
Usernames have not changed. The only difference between my old forums users and my new is that my admin password changed and I registered a test account in Xenforo. Other than that there have been no changes.
Maybe what I will do is make a new category and move the data from the duplicated category into that and then delete the duplicated category.