Me too.

I discoverd the problem and fixed it. The robots txt. was the problem.

I was blocking tag links, these tag links are seen by Google a duplicate content. I was using Disallow in front of the of the link. Wrong: It must be Allow!

It is funky, and really illogical to me=

Here is the way to use it.

Disallow = spider it
Allow = Don't Spider it

After correcting my Robots txt file I tested the new file in Webmaster Tools. The return of the test was 200, allowed, and it remove this line "Detected as a directory; specific files may have different restrictions".

So, by changing from Disallow to Allow I have removed a bunch of duplicate content from my blog.

Your website is a directory. It has folders and files.