We are having a very unusual issue of slowly disappearing categories. The order of events is sort of in this order.
1. Everything is fine and dandy after we updated to 3.1.1.
2. In the list view of posts, under the categories column, we only see 'uncategorized'.
In edit and quick edit, we can see that they ARE categorized, and we can see there are categories in the filter tool. On the site itself, clicking the category buttons give us 'there are no posts here (yet)' or similar.
3. Everything becomes totally uncategorized (even in edit views) and the filter tool shows no categories. However, on the dashboard, there are supposedly 9 categories. On the category admin page, there is nothing listed.
Deactivating all plugins has not worked. Reinstalling wordpress has not worked.
The wp export file has no categories on it, we uploaded it to another blog.
Installing the wordpress application on a fresh subdomain (new database, new user, etc) eventually has the same issue after updating to 3.1.1, when the wp export file is loaded and new categories are assigned. The new categories eventually 'disappear'.
Recreating the entire site (new database, new user, etc) on the same domain has the same result.
Note: In the dashboard, we can always see there are as many categories as we have created. If we try to create a category with the slug of one that we created before, that is denied even though there are no listed categories.
Obviously something is being screwed up in the database or WP's code, but we don't know exactly how to fix it other than reinstall everything and NOT update wordpress.