I have more than one domain hosted at the same ISP. For instance, call my primary URL http://www.primary.com and my secondary URL http://www.secondary.com.
All of my files are actually located in a subdirectory of http://www.primary.com named http://www.secondary.com. So the following two URLs are actually the same place:
http://www.secondary.com/blog
http://www.primary.com/www.secondary.com/blog
When I first navigate to my blog and type the first URL, it is being replaced with the second URL. The strange thing is that when I select a comment, permalink or category, it uses the first URL form (which is much more desirable from my perspective).
I'm not a great coder, but I could probably make some sort of basic hack if someone could point me to the right location to look. It happens when you first navigate to the blog or any time you click on the header to return to the home page.
The whole admin module always has the second form of the URL. It only seems to occur at the topmost page.