Amtrak terms and conditions state that if you fail to board your train as booked your entire reservation is subject to cancellation 

It's one of the first things detailed on the conditions of carriage page here.

http://www.amtrak.com/servlet/ContentServer?c=Page&pagename=am%2FLayout&cid=1241337896121 

If discovered that you boarded at the wrong station the conductor at the very least might ask you to pay the difference in fare, and possibly be forced purchase a whole new ticket.