I have a long standing problem with the panel menus top and scroll bars disappearing. This happened in CS5 and still occurs in CS6 for me. I use a Mac Pro hexacore with three monitors (two video cards). It occurs after placing a document or switching from another app. Resetting prefs does not help. The work around is to reset the workspace or hit the tab key twice to redraw the palettes or click on the finder and back on an ID window. I leave lots of panels open on the right secondary screen with the main interface on the primary screen and misc. on the left screen. No issues like this in other apps.
Message was edited for clarity