I think that’s the problem – something to do with deleting custom taxonomies when there are links in the Nav Menu which link to/are related to those now-missing taxonomies.
I read a post somewhere describing the exact problem, and this guy had spent a considerable amount of time trying to fix the problem without success. In the end he had fixed it by resetting WP back to a clean state (I assume a default database), which will of course result in complete loss of site data.
I would imagine there’s a fix by delving into the database, but I’ve not explored this as the error I had was none-critical (on a localhost test site).
