I want to be sure I understand you correctly. Are you saying, you choose
restart from the shutdown menu, the system restarts and the Start menu is
still open? Have you tried shutting the computer down completely, waiting a
few minutes and then booting the system.
If that resolves the issue, once booted, right click the Start button,
select properties, go to the Start Menu tab, place a check next to "Classic
Start menu." This will give you a scrolling start menu as opposed to the
"fly out" extended menu and should prevent the issue in the future.