Java deployment Toolkit adds a hidden embed element to the page when you deploy a javafx applet.
When I have a DOCTYPE declaration into the page, the browser seems to add whitespace around this embed element due to being more strict.
The problem is easily reproducible when the Html page is larger than the viewport (i.e. you need to scroll).... now, include the dtjava.js at the bottom of the page -> Result whitespace is added at the bottom

The workaround is to explicitly set the display CSS property to none:

#dtjavaPlugin { display: none; }