I've lost a lot of my accessory windows from some random app install
So it turns out that these two links sent me on my way. Doing a self post in case other people can find my post by googling.

Unresponsive save dialogs in Preview  

http://lists.apple.com/archives/macos-x-server/2012/Aug/msg00291.html

To fix this: Disable "Documents and Data" under System Preferences > iCloud and you're on your way.

This has to be the most aggravating bug I've found in a while. Ugh.