But what I really want to know is whether it's a redirect issue or a tool issue. If you use something like LiveHeaders (Firefox, there are probably equivalents for other browsers) do all four URLs report 301 responses? If so, what are they all getting redirected to? 1 and 2 can't redirect to each other, or you'd be getting an infinite loop.
I don't think there's any problem with the Tools because I checked for my other sites and it's fine. Yes 1 and 2 can't redirect each other. But it's showing 301 for all the urls.
Btw one thing I found in htaccess file that there's no redirection code for domain but for blog of the same [domain.com/blog.html].