You are absolutely correct Colin. The issue is, I believe, that when I switched software platforms, Xenforo does a 301 redirect from the old vbulletin style urls to the Xenforo urls. It holds a database of every single vBulletin url from the old board, but that 301 redirect is, perhaps, the issue. Google stays nicely opaque on the issue of 301 redirects and I believe I discussed this in conversations over whether or not to switch software platforms. You can probably search for the thread where I talk about this. My fear was that when you do a 301 redirect, you lose a little oomph from that link juice. Since we have 10K+ links coming in, we lose lots of little oomphs which equals the loss of a big oomph!
Estimates are that you lose 5 to 10% of link juice for a 301 redirect, although SEO's debate how much all the time. Google has many factors that determine how to rank webpages. SEO's know many of them, but they are unsure of the weights of each, and there are no doubt a bunch of hidden ones too.
My rationale on switching platforms was that we are risking losing some visitors in return for hopefully a site that has a better user experience. The idea is that over the longer term, I hope we recover some/all/more visitors, while improving the experience and having greater security. What has surprised me is that the time on site figure has gone down slightly. I don't know if that is because the site is faster so people get their answers more rapidly, or something else. The old site was significantly slower so perhaps it is that, who knows for sure.
Post count here has gone up. My brain tells me that Google might consider newer software to be better and so rank extra for that, but maybe I am getting ahead of myself there.