I have a couple of directories and since the Penguin update, I have had several requests for removal because
"We've reviewed your site and we still see links to your site that violate our quality guidelines. Specifically, look for possibly artificial or unnatural links pointing to your site that could be intended to manipulate PageRank. Examples of unnatural linking could include buying links to pass PageRank or participating in link schemes."
Now I have sites in the same directory and once I added a couple to the GWT's I have not had that same warning, so what's the deal? Is my directory giving off the warning or are the sites that have received the warning getting the warnings, but those warnings don't actually tell them which links are bad?

Anyone use GWT and can shed some light on this?