I am having a problem similar to http://support.semicolonweb.com/forums/topic/local-links-to-sections/ but couldn't resolve it with the method proposed.
When clicking a link to a section in the header navigation (example Travel lodging) the resulting is "too high" with the top of the section cut off at the top.
However, the link to the section in the green-blue submenu (which is on all pages except index) goes to the correct location on the page.
The website: http://www.math.vt.edu/people/gugercin/householder/index.html
Thank you so much!
