Hi, I'm having the same issue.
I didn't do any rearranging, but one day my 3rd monitor stopped working.
2 monitors plugged in via DVI
1 monitor via Active mini DisplayPort adapter
This started about a month ago - I had the issue about a week before I went on vacation, then I got back and moved to a new home. I'm just now getting around to setting everything up again and still running into this issue.
I'm unaware of any updating that occured. The adapter still allows the monitor to be used, but receive the "To extend the desktop, a desktop or display must be disabled" message only allowing 2 at a time.