ColourOfSpring - 4:13 pm on Apr 11, 2013 (gmt 0)
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.
Not to hijack this thread, but thanks for your reply Marie. The site got hit back in March 2012 as part of the "sting operation" Google did on a number of blog networks. I had used one network just for a few weeks before it got rumbled by Google. The entire blog network was taken offline soon after so my links disappeared with the network. I'd also linked to this site from a couple of sites I own - I removed those links. It was a new site with no 301'd redirections pointing to it. To be honest, it wasn't really ranking well anyway, but I obviously had plans for this site, so I persevered with the RRs to Google, and they batted them right back to me saying there were still links. At the time GWT didn't report any links I didn't know about, but they DID still show those old links that were removed (I know GWT takes time to update though). I would have thought that Google would recrawl those links after an RR to see that I wasn't just lying. Again though, perhaps there were some links that no tool could find, and GWT also didn't report about.