Due to the limitations of "Arrow" (the reservation system used by Amtrak), each "train" must be sold separately (and thus may have different fares.
The situation is similar to the airlines. (I'm just making up these flight numbers, but you get the idea.) A flight from JFK to Chicago may be listed as United #173, Qantas #2849, US Airways #4573, Lufthansa #6352 and other airline flight numbers. If you call each airline for a seat on the plane, you will very likely get a different fare from each airline! Even though they are all selling a seat on the very same plane! Each "flight" is offered at a different fare.