Ah, on Mac. I'm PC, and I don't know whether I can use your project folder. In any event, in the zipped file is the project file and a folder "_MACOSX" - inside that is "._xxx" where xxx is the project with .ncor extension. But no size.
In any event, my first test is the menu. The only problem I see is the buttons are far to the side, and by the time Encore modifies to DVD size, this can cause problems. But they are usually with the appearance of highlights. But I wonder.
I used the menu in a small project, but I see no jumping or shifts.
If you create a test version of your project with the menu and one timeline, remove all but the "Whale Rock" button and link that to the timeline, do you see the problem?