First to explain the issue facing some directories ...
When we search for a directory on Google's site using
www.domain.com most directories will come up as the first search result.
However if enclosed in quotes "www.domain.com" many directories are NOT in the first result. Often these directories do not appear for targetted keywords in the first 30 or 40 results. Some people are also noting a drop in the number of indexed pages.
This has led some people to speculate there is a error in Google's reults OR there has been a penalty applied.
The sites are NOT banned since they appear in the index when searching for their domain name. For the most part page rank has remained unchanged, where a banned site will usually show a gray bar.
So the big question --- "what is going on here?"