When I saved the file with a different name, the layout problem went away. I must have changed something where I didn't understand what else it was doing and that went away with the re-save. I don't know if I immediately have the patience to try repeating the process, since it is working on the re-save. If it comes up again, I'll let you know, but it was a brief "bug", I'm sure was actually happening, but probably more related to me over-fidgeting with settings.
On a different note, as far as labeling the interval distances after 'staff note-jumps', it may be good if I just do that with an exported pdf in Inkscape, and avoid trying to set up something with automatic text, since alignment issues would most likely be frustrating (the other thing is: printing text on both display and print view... really, the numerical visual aid is useful for counterpoint writing in perhaps the early phases to help the student make sure they are following certain rules, so wouldn't necessarily need to be printed on the score itself; But as I said, I will try Inkscape for that.