smallcompany - 5:05 pm on Nov 4, 2012 (gmt 0)

I set up redirects through .htaccess to keep the back links and page rank.

What did you do for this exactly? Sometimes technical mistakes block or direct search engines to a wrong direction.
If it was as simple as you've described - from subfolder to the root of your domain - you should be able to achieve it with a single line in your .htaccess.
Also, have you checked what G says for your robots.txt in WMT?