score:9
Like many airlines today, Amtrak's loyalty program is fundamentally based on ticket price, not miles. Specifically, you receive 2 points per dollar. You mentioned your wife is a senior citizen, which entitles her to a 10% discount. Because her ticket was 10% cheaper, she received 10% less points.
Note that the senior discount is not applicable with any other discount and certain premium seating. The other fares were likely ineligible for the senior discount.