Any idea what would cause this? I've even gone as far as creating a new browser profile and the issue persists.
We've had another Admin complain about the same issue and it cleared up "magically" after a day or so.
Try going to <url>/install/ and reimporting the master data.
The screenshot doesn't appear to show all permissions, on the basis that languages and styles aren't showing, but you should have permissions for at least some things. (And there should always be some links that aren't permission controlled.)
If that doesn't sort it, I think you'd need to start looking at add-ons (which may edit the available entries or be using a template modification to change them).