clockspot

I’m a little late to the party, but if you still need help, here’s my two cents –

I ran into this issue, and in my case, the problem was that WordPress’ database user didn’t have sufficient privileges to alter the structure of the database, so the upgrades weren’t quite going through.

So I gave the user structure-altering privileges (create, drop, alter, etc) and forced a database upgrade, and my previously missing categories came right back.

I had this problem and solved it today. As MichaelH suspected, it was an upgrade problem – it turned out my WordPress database user didn’t have enough privileges to complete the upgrades.

In my case, I hadn’t lost my categories; they were still in the old wp_categories table, which was supposed to have been replaced with the trio of wp_term tables somewhere along the line. The thing was, even though I had upgraded, WordPress hadn’t changed the database structure.

So I gave its database user privileges to alter the structure (create, drop, alter, etc) and forced a database upgrade as above, and it worked! My categories are once again listed in the admin panel and my posts still belong to them.

I hope that helps!