I resolved this problem: to optimize theme loading Vaadin use a gwt theme loader wich load css, images,etc… client side with the js compiled file, so it override your application theme. to disable this behavior you have to create a custom theme loader and override the load method and leave it empty. this issue was solved at this forum thread
https://vaadin.com/forum/#!/thread/4909752/7867897 by Jouni Koivuviita.