It's not often I post a new thread here but I'm in need of any ideas with an issue I've got.
This happens on all sites (it's a v3.2.1 Multisite) with all post types (one of the sites uses MarketPress and the same happens with products).
The posts are in the database, visible on the frontend and editable so long as you can find your way to the edit post page.
I took the site offline, deactivate all plugins (both per-site and network), switched to Twenty Ten on all sites and de-activated mu-plugins (just domain mapping).
I've checked the database and there are only two accounts (those two correctly listed) with a wp_user_level of 10. The next level down held by anyone is a 7. wp_capabilities also correctly indicates administrator for only those two accounts.
The whole network is now bare - there is nothing that isn't out-of-the-box WordPress, it's like a fresh install.
*tears hair out onto keyboard*