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ColourOfSpring...for your site that you removed all of your links I have a few thoughts. Did you download your links from WMT? If there were links that only Google could see then they would be in there. Is it possible that you had any sites redirecting to this one? If those sites had unnatural links then they could pass the penalty on. And thirdly, are you positive that the warning mentioned links? Sometimes Google can give penalties for on-page issues as well.
the webspam team employee that reviews your site will look at some of the links that they have flagged as unnatural and then see if you've been able to remove any.
They check the links manually? Are you sure about this?
Google does not show any backlinks in the webmaster tool since the unnatural links warning came several months ago.
On the disavow list, do you have to include only the top level domain or every link coming from the particular domain?