mihomes - 7:08 am on Oct 23, 2013 (gmt 0)
Shai... good point. You will want to make sure you have the www version set as preferred in WMT as well as a 301 in your htaccess to www. I just assumed this.
Make sure you update the thread so we know how this turned out. In the past I have noticed little things like the screenshot image not updating on my non-preferred domain in WMT and this may be the same case with your penalty removal. Maybe they queue the non-preferred updates rather than them being automatic? You might also want to make sure the page isn't cached somehow in your browser (I think I remember something like that happening to me in WMT as well).