Does it occur with one precise JavaFX application ?
I suspect the coordinates of the top left corner of the application window are persisted but corrupted then at the next restart the process starts up and you see nothing.
SceneBuilder 2.0 is hit by such an issue (see https://javafx-jira.kenai.com/browse/DTL-6731), work around is to clean yourself the corrupted value.
Hope this helps
Thanks this looks to be in scene builder. So how do I clean this from within a JavaFX application that is not scene builder?