You could always fully qualify the link with the domain name as well.
<a href="http://sitename.com/Default.aspx">Home</a>
<a href="http://sitename.com/AboutUs.aspx">About Us</a>
<a href="http://sitename.com/Secure_Page/Products.aspx">Products</a>
or in the code behind for the masterpage you could have it write out that block with a ../ added if you are in the subfolder. The links could always just be generated in the code behind and you can customise them how you want.
Good Luck.