The Altera® device development kit (Board Test System (BTS), CLK, and Power) GUIs heavily rely on the Quartus® II software version due to specific library requirements.
Unlike other Altera development tools, the GUI for the development kits does not have a relative path relationship to the Quartus II software, in some cases, you will need to set the path manually.
You can download this How-To: Setting up the environment variable for the development kit GUIs document that will help guide you in checking for the path settings and if required it will also show you how to set the paths.