Amfleet,
First you can't request other rooms within the same car, as they would all be the same price, at least within the categories of Deluxe & Standard. You could try getting the same sized room in a different car. However, I think that Amtrak's system always brings up the cheapest room available so I wouldn't be surprised if you get a higher fare when they try that.
Now as for the huge jump in price, it really does sound like you got something wrong in that one request. However as you know the prices do rise as the train fills up.
Case in point, my recent trip on the AT to Florida. For my journey down with part of my family, I cashed in some of my Guest Rewards points. Coming back however, we were traveling on a holiday weekend so I couldn't do that. When my family and I first started talking about making this trip, I had priced out our return trip on Memorial Day weekend. For one van, 4 adults, 1 child in two deluxe bedrooms I was given a price of $1,279 in early February.
Thanks to some planning issues and some procrastination, I didn't book the tickets for over a month. Finally with everything resolved, I was ready to book the return by mid March. I checked on Saturday the 8th of March and the price was still $1,279 but I decided to wait until a billing cycle on my credit card closed the next day on Sunday. This way I could postpone paying the bill for another month.
On Sunday night I checked again and the price had jumped by 60 bucks to $1,339. However I didn't feel like getting up to get my card at that time, much less actually calling Amtrak on the phone. I needed to call since I could not book two adjoining deluxe rooms via the net. I resolved to call the very next day on the 10th before the price went up any more.
Well that was a big mistake; by the time I called Amtrak on Monday afternoon the price had really jumped. I ended up paying $1,605 for our return trip. By delaying I ended up paying an extra $371, all because I wanted to hit next months bill. Ouch!
The bottom line is once Amtrak meets the minimum threshold of rooms booked; watch out. All it takes is one more person to book a room and there go the prices.