The issue is IIS is configured to have a sub application. If you look in IIS you'll see the "Default website" (most likely" and an application directory called "Kentico" under it, then the CMS directiry is where the actual website code resides.
What you need to do is update that "Default website" OR create a new website and name it what you want and point to the CMS directory on the servers hard drive so it will serve the site up from the root /CMS directory without having the virtual directory.
See this post as well for a reference:
https://devnet.kentico.com/questions/remove-sitename-from-site-urls