Hi,
If you are talking about the auto generated links like in the toolbar, you should just specify say "page1.html" instead of "
http://something/page1.html" in the toolbar table of website settings.
Similarly for links to pages within the erpnext generated website, you just need to specify the page name in the href part and not the whole url.
Hope this clarifies the issue. Else let us know the url of the website so that we can check it out. Our website is not facing this issue, hence we are not sure if it is related to the product or your specifications of url.
Thanks,
Anand.