SharePoint 2010 apparently has a hidden issue between SharePoint publishing and Top Links and Master Pages.  There is no way that one can manage Master Pages and Top Links the same time.  Whenever the publishing features of SharePoint are enabled, Top Links administration would be hidden, while disabling publishing features would disable the management of master pages.

To enable Top Link administration, here are the steps:

  1. Go to Site Actions -> Site Settings
  2. Choose Manage Site Features under Site Actions
  3. Disable “SharePoint Server Publishing”
  4. Choose Site Actions -> Site Settings
  5. Choose Site Collection Features under Site Collection Administration
  6. Disable “SharePoint Server Publishing Infrastructure
  7. Now, “Top Link” link magically reappears under Site Settings.

However, the story is not over yet.  When managing Top Links, not all the links would make to the top bar even though they appear in the Top Link administration.  What happened was that, any new links created after the publishing features were enabled would become “phantom entries” where they only appear in the administration screen.  To display them, administrator would have to manually create the links.

Update: Microsoft acknowledges such issue in their Knowledge Base.