Maybe a user accidentally removed the appointment? This is very easy to do since once you click remove, the program doesn't ask "are you sure?" or anything like that. And after it's removed there's no way to track if a patient ever had an appointment at that time. This happens to us occasionally and is the most likely explanation when someone comes in with an appointment card and no appointment in AC.
For me, there is a "document a changed appointment" window that pops up when you try to delete or remove a program. Not sure if this is something that can be turned on or off, but that might be part an issue if it's not working on your setup.
YES, there is an box in the user preferences (control + U from the main screen or under the Edit menu my preferences, user preferences) that will turn this back on.
