You looked and watched every car throughout the whole trip? You didn't sleep more than an hour or so and walked the train after each stop?
Doesn't sound like a forum manager caliber post. If you have an explanation for what HARHBG experienced, let's hear it.
Moving roomettes costing $128: customer service rep not trained on how to switch room without forcing change in fare. Fare for roomette was higher on day of departure than on day ticket was purchased.
Bedrooms significantly higher: again, higher cost bucket for bedrooms.
Bedrooms looking open throughout trip: possible that most rooms were sold over a portion of the trip, and HARHBG saw them open at the beginning and end of the trip (or, potentially, saw some bedrooms open at the beginning of the trip and some other bedrooms open at the end of the trip.) Between times that HARHBG checked, some rooms were sold and occupied (perhaps during times when HARHBG was in their room or sleeping, and thus not checking whether these rooms were occupied.)
Now based on the fact they could be sold, there was at least one empty roomette and one empty bedroom the whole way. There may have been more, and it's possible that there were a lot. But even someone on the train, unless they're taking very good stock at the situation on board throughout the trip (including overnight hours,) may not see every room change and use of rooms, and the rooms may have been more sold than a simple walk through of the train could account for.
The roomette room change costing more is likely improper training and should be escalated to a supervisor as needed. However, it would also make sense to talk with the SCA and see if a room change is possible, especially if a call to customer service is leading to a dead end. I would hope Amtrak trains SCAs on the procedure for doing so, as it seems that it would be a situation that would come up enough to train on.
Whatever the stock of rooms were on the train, as long as there was another roomette open the entire ticketed distance (which I assume there was, based on the fact the room could still be purchased) on board personnel should be able to make that change if a passenger needs to make that change due to an issue with the room (and a screaming child next door should be enough for that change to be made.) However, it's possible that there's other reasons why the cost to upgrade to a bedroom was so high even though bedrooms appeared open throughout the trip than simply that Amtrak can't properly manage pricing for rooms.