Could you tell me which table I need to check and how many/which values should be there?
Update: as I should mention, I do have access to all items that should be in the menu
e.g. if I type /index.php?p=layout I get the layout overview, if I type /index.php?p=user I get the user configuration.
I can also change the settings on these pages, so it is not a permission problem.