Why do the character elements change position in the different throughlines?
My understanding from the Theory Book and all the examples I've seen shows the Motivational Quads with Consider/Logic/Feeling/Reconsider in the top left quad, and the others played out accordingly. After completing my storyform, the top-left quad looks like this: Consider/Pursuit/Avoidance/Reconsider, with other changes accordingly. The replacement of Logic by Pursuit and Feeling by Avoidance is throwing me. Is this what is supposed to happen after I complete a storyform?
The arrangement of the elements is different in each of the four throughlines/domains. For the sake of consistency, the arrangement we usually show in the book and reference material is the arrangement found in the Activities class. The arrangement you describe for your story suggests that your Overall Story Throughline is in the Fixed Attitude class.
In other words, Dramatica shows you the arrangement (and groupings) of the story elements appropriate to your Overall Story Throughline's domain.