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The root URL, [domain.sth...] is not indexed - even direct query about the url doesn't show anything. Googlebot visits this URL at least once a day, follows and indexes all links on this page. There are inbound links to the root url, both from this domain and from other domains, both from the same IP and from different C blocks.
Moreover, just recently I entered one of these sites into DMOZ. In the according DMOZ subcategory, there are 7 entries including my site. But in Google Directory, when I was looking for the same subcategory, I found something very weird. One level before the subcategory, my subcategory was listed "fluffy widget theories (7)". When I entered it, there are only six entries, with my site missing!
Is this enough to think it's a penalty? G has indexed tens of subpages from this domain, only the root URL is missing. I used to have randomly changing images on that page, maybe it was considered cloaking? Is this situation enough to contact email@example.com?