Was it the same train and date for each segment of the multi-segment ticket? As noted above, sometimes, due to a glitch in Amtrak's system, even if you request the same train on all segments, the computer will spit out different trains, and price the ticket accordingly. If one of those trains has different seat availability than the others, you might end up with a higher fare than if you were able to book all segments on the same train. A multi-segment ticket on a single train should price the same as a single-segment ticket with the same starting and ending cities.