I am launching JavaFX applet (size 1000 X 703) from browser using Java Script Windows.open method (code given below).
The applet is getting truncated if the browser zoom is less than 100%. My applet stage size is 1000 X 703 also.
Not sure if it will help, but the Ensemble application has some kind of setup where it is able to fill the entire browser window (including when the window is resized). You might want to look at the Ensemble source to see how that is done and adapt that to your application.