From my experience, there is no pattern to the hares. I have seen them change several times in a day. I've also seen different fares for the same accommodations on the same train. On the Texas Eagle, if you look at sleepers on train 422, you might see a different fare than train 22.
I've observed much the same as you have. And the following shows, I think, the incongruity you noted between the Texas Eagle and the Sunset Limited:
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I defy anyone to explain that one by invoking buckets, yield management or any other mumbo jumbo. One explanation I
can understand is a blind (and possibly rabid) monkey is picking fares for Amtrak. While I know full well that's not really how fares are set - it may as well be as far as I can see.