petehall - 12:28 pm on May 4, 2013 (gmt 0)
I would actually wonder more about internal links and text. Does the particular site you're referring to use more "matching text" in internal links or on page than the others you have that are not affected do?
I did a complete re-design of the site some time ago, and as such there is very little in way of optimised anchor text within the site. The only thing this can be (in my mind anyway) is the domain or anchor text of incoming links (likely a combination).
Something to bear in mind with regards to the EMD, is that I think it's a bit of a 'red herring' as we'd say in the UK. Every single domain name registered is actually an EMD, however if the domain is not directly related to a product (money term) then it's unlikely others will be competing for it. I'm sure it's something related to the level of competition of the term and most sites will scrape by without any issues.
Perhaps the EMD just tips the balance of over optimisation and removing this from the equation helps? Either that or it's a direct result from exact match anchor text from other sites, which is a side effect of having an aged EMD. However if that were the case I think it would be affecting company name searches and wreaking havoc across the index.