I have changed some minor things in the UI using the HTML Tool. But everytime I close reopen it nothing is saved!

You mean the html tool when you run a game? You can only change styles there temporarily but it does not save them in your game. The main function of the tool is to show which styles are active. To change these values you must code them in a script. Have a look at http://textadventures.co.uk/forum/samples/topic/5111/how-to-modify-the-user-interface