We have several country specific sites set up as folders of our main domain. We use hreflang tags to get the relevant site served in each country, with mixed success. In about 60% of searches the US site appears.
Beginning in late October our rankings for the US have slowly, but reasonably steadily dropped. Each week we'll see 10 or so keyword rises and 15-30 keywords drop. Generally by 1-3 places. This is much more movement than we were seeing in the months prior to this.
Is this a result of penguin, or just coincidence? The US subfolder is the only one which has seen drops overall, the rest have actually improved slightly during this time period. I would expect any impact due to Penguin to effect the whole domain?
I've been checking through our backlinks and we do a have a handful of bad links, along with a 100 or so which look a little odd and not completely relevant. I have contacted sites and had some of these removed, and created a disavow list with the worst of the rest. I haven't asked for the site to be re-considered yet.
We haven't had any message in webmaster tools re: bad links or similar.
Cheers.