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Could permanent redirect affect SEO?

A friend of mine has his site at domain.com. He, because of a framework and blah blah blah, has allocated the content inside a folder named /home. So, if you go to domain.com it does a redirect to domain.com/home. It is a permanent redirect.

Now, when I go to Google, Bing, Yahoo Search, etc, and look for "site:domain.com" no pages are listed but the domain.com page and there is no page there actually (the page is inside /home).

Can the permanent redirect be the reason why no pages inside /home are indexed?

If you need to look inside the site let me know so I let the real domain here. Thank you!

EDIT:

I've went through the index status report at Google WebMaster tools and I get this report by today. Does it say anything interesting?

Ever crawled: 2,874 Total indexed: 2 Blocked by robots: 1 Removed: 0