The reason why the menu is not displaying correctly on the principal page is because of the path to the IE specific CSS and other resources. The page is looking for the IE css file here:
It is looking starting in the current principal directory. You will need to adjust the paths on this page so that it is like the index page in the franklin directory. Adding in a ../ in front of the path should do it. If this is in a template page the paths in the IE conditional comments do not get adjusted, you will need to do that manually in the template.