Hi Jeremy,
as it is a fresh installation (debian+lamp+wordpress from the apt resources) there is only "Akismet" and "Jetpack" as Plugins and the theme is "Twenty Twelve". I made no further configuration (permalinks or something else).
You can take a look at here and here.
It's no problem to test, because I will rebuild this site completely in future.
Hope this helps to find a solution.
Peter