One of my sites is listed twice in LinkMachine's Site Manager. Why?

When the URL for linkmachine.php for a LinkMachine installation is changed (under Site Settings), sometimes this will result in that one installation being counted more than once, and taking up multiple site licenses. This can cause the installation to be listed multiple times in the Site Manager, and can prevent you from making use of all your site licenses, because more than one is taken up by the same installation. If this is the case, click on the X in the Remove column for all instances of the duplicated site in the Site Manager. The next time you use that LinkMachine installation it will be re-added to the Site Manager list using just the current, correct URL.