Hugh / Sgt,
Been exactly there and done that. Track my posts in one thread on here around mid-July 2013. As I realized then, your problem is more than likely NOT that they think you are about another niche subject, so much as they WILL NOT ALLOW YOU TO RANK FOR KEYWORDS IN/INCLUDING YOUR PRIMARY NICHE. Thus it looks like they have you in the wrong niche. Like Sgt mentioned, they pick up on all the secondary topics, which in our case, just like his, included tangential topics. I call it an "anti-authority penalty", where your site is so concentrated on the one topic that maybe they think you are trying to game them and thus lock you out of it (even though you may have BEEN the original authority for many years before G existed). If you look in that thread you'll see I was not the only one who came out of it back in July (fortunately). As far as how or why I can't shed much light on it beyond what was mentioned in the thread.
I did notice you also did some 301 redirs which we also had to do. Our site was split across 3 different domains for load balancing reasons (in the old days 90's that was the cheapest way unless you wanted to pay 10x as much to simply double your bandwidth) and we slowly moved a few pages at a time to the 1 primary page. Perhaps this makes them think you are trying to transfer PR from bought sites (even if you owned them all to begin with).
I spent 2 years of my life, that could probably have been much better spent bettering humanity and the website, trying to unravel it. Don't know if anything I did in that time made a lick of difference. But look at your site in that light and at least it may make more sense. I know it is extremely frustrating and they should be more sensitive to fixing the problem.