I had a similar problem: after the (painful) move to Mountain Lion two months ago, I had managed to make Safari download pdfs instead of displaying them, and then today, after a simple restart, Safari began to display pdfs in a separate window.
Your solution got me back to where I wanted to be. I have added it to the very long list of tweaks I need to make ML productive.
I have no clue which piece of software installed those plugins behind my back.
Thanks so much,