Initialize Javascript in Frameless Layout when new page loads

I'm Experiencing problems when  trying to add some Javascript functions to my RoboHelp Page.

Script references are ignored when deploying the project on the web server.

I found out the following connection:

If Frameless output  is hosted on the server then full page doesn't reload every time only the topic area reloads same as Responsive output. Also all scripts in header area or in other places seem to be ignored.

My Question: Is there a way to initialize Javascript code every time when a new page is loaded even when the Project is hosted on the server?

Adding the script to the start page does not help, because I want to initialize the class on every page.

As mentioned everything works fine in the Robohelp Preview.

Perhaps the user should be informed that there is a difference in the behaviour between the Preview in Robohelp and behaviour on the web server.

Thanks in advance for any help.