I'm just as confused. The featured image metabox disappears across all post types and pages, and the option doesn't show up in the screen options. I've deactivated all plugins and tried each one at a time. I even removed my custom post types, extra JS files, etc to see if something there was causing it.
The theme is based on the Bones theme, and I use several plugins like Advanced Custom Fields, Post 2 Post, AIOSEO and Advanced Recent Post Widget. I can't rule out something in my code, but AIOSEO is the only plugin that affects it directly with activation/deactivation.
Strange stuff. Just thought I'd check to see if you've had this before.