On and off, Aquamacs starts behaving strangely with the line wrap. I usually have word-wrap mode set. And yet, when I open an org-mode file I see that truncate-mode or some other such is set. Here is what to do to get it back to normal:
Go to Options -> Customize Aquamacs -> Aquamacs-specific options. That will open up a buffer with a bunch of options. Scroll down to ‘Text mode hook’. Unselect all the options, select set-word-wrap and delete all the extra options set at the bottom, if any. Save for all sessions.