Really can't think of any reason this should happen. I would be sure the layering is correct in the left pane and not depend on "Always on top". Maybe try both. When you click the ones that do NOT show, does it take you to that page? If so, then the layering is correct.
I would be glad to look at that page. If you can't send me the whole course (File undefined Zip) then how about just one page. Copy the page and paste into a new title. It won't work but I can fix that. I want to see exactly what you have.