Last week I built a download page for a free pdf ebook in a sub-directory on my server. At the bottom of the page, I inserted the URL to my primary webpage in the main directory (the original domain name).
When I tested it, it took me to the index page in the subdirectory!

I checked the html, but there wasn't a clue as to why this was happening. After an hour of experimentation, I finally had to assign a hyperlink through mytinyurl to take it out of the subdirectory. So, if anyone has had this problem, this is one way to make it work.
Any other ideas?