That's because they're using expected demand for tickets 11 months out. It's not a simple "first x rooms at low bucket, second x rooms at second bucket, etc." They can look back at previous years and see what the demand trend historically has been, and err a bit on the side of a bit too high in case it happens to be more popular (and they can sell more rooms at a higher price.) If they don't sell as many rooms as they expect, then they'll lower the price a few months in to try and fill more rooms, adjusting as needed based on room sales and any other demand indicators from previous years. For example, they might keep holidays at a higher price even if rooms haven't sold yet, as they can see from previous years that they'll sell out closer in at higher prices.
Airlines do the same thing, just on a much more advanced scale than Amtrak. It's rarely the absolute cheapest to book when tickets are first released; they're either at a placeholder price (if they wanted to release the schedule but revenue management hasn't fine-tuned it yet) or the price that they can expect to get early bookers to pay. After all, if the price is only $20 more than the sale price, why wait and risk that sale never happening, or that sale applying to a less desired flight? As time goes on, they'll adjust some prices down (where they aren't getting as many sales) and others up (where sales are going strong.)