I have a similar problem. I have a file head.php which contains all the links to css files and script files (basically everything that goes in the <head> tag).
If I include that file in two pages, one in the root folder and one in a subfolder, the one in the subfolder will not be referenced properly since the link to the css file is relative to the root folder:
<link type="text/css" src="css/style.css" />
Adding the '/' to the front of the filepath does not resolve the issue in this case.
