If I put Youtube to fullscreen on a secondary display, the menu bar is hidden on the primary screen (the dock stays there) if Safari is the active application. If I cmd-tab to another application, the menu bar appears. IMHO this shouldn't be the case. Also, a small UX thing - I understand that generally new Safari windows (created by either cmd-N or clicking a link in some app) are put on the same screen as the last one, but in case the last one was put to full screen and another screen exists, I think this should be preferred. Use case - I quite often open full live concert videos on Youtube and put them playing fullscreen for "background" on my secondary screen (which is the laptop display when my laptop is connected to an external Cinema Display).
Are you using HTML5 or Flash with YouTube? How exactly do you make it full screen. You did not specify your OS version. Is it OS X 10.8.2? > in case the last one was put to full screen and another screen exists, I think this should be preferred. Please file a separate bug for each issue. This one is a Safari one, so please file it via <http://bugreport.apple.com>, not the WebKit Bugzilla.
This will be fixed by bug #100025. At issue is the use of -[NSApp setPresentationOptions:], which sets auto-hide values for the dock and menu on a application-global basis. Marking as dup. *** This bug has been marked as a duplicate of bug 100025 ***