To be more specific, ClearCase doesn't appear in the menus. If you go to Window | Perspective |Custom Perspective and select the Command Groups Availability you see ClearCase and ClearCaseActivitiy (both unchecked). Check them and go to the first tab, Tool Bar Visibility and ClearCase appears checked. Click the OK button and nothing happens. Click the Cancel and the dialog goes away.
Window 7, Flash Builder 4.0, ClearCase 8
I run Flex as Administrator in case that made a difference.