Not sure if you already got an answer for this, but I finally figured it out (cuz it was bothering the crap out of me).
Uncheck Preferences > Security (Enhanced) > Enable Protected Mode at startup.
BTW, I noticed that when protected mode is in play, it sets the permissions to what you have in your personal Users folder, no matter where the pdf is on your machine. If you are editing a pdf on a network share, it doesn't do this.