You should NOT be publishing to FlashVR (swf) for website display.
You should be publishing to FlashVR. Fullscreen option requires a HTML page with the parameter AllowFullScreen = "true" without the HTML page you will not get fullscreen.
FlashVR (exe) = self contained designed for CD rom or email.
FlashVR (swf) = Designed for use with Flash CS (Flash Developer) or local viewing via Flash standalone player.
FlashVR = For online website display