Ian,
Very sorry for the delay. I poked around your site a bit tonight. The first thing I noticed, and fixed, was that the JFBConnect User plugin was ordered before the Joomla User plugin. I fixed that, and then did some testing.
It wass strange what I was seeing, so maybe you can confirm some things. I registered multiple times and then would delete my account after changing some settings and registering again. In all cases, after registering, if I went to the "My Profile" link, Community Builder seemed to indicate that I wasn't approved and that I hadn't verified my email address. This was regardless of the "Skip CB Activation" setting in the JFBC profile plugin, which is supposed to automatically approve the user.
In all cases, my user did seem to be properly logged in and if I hit the Forum link, it would say "Logout [sourcecoast]", which indicates the bridge there was working properly. Also, when I deleted my account (in the Joomla User Manager), there was a notice that the PHPBB user was also being deleted.
So, it seems (to me) that the bridge portion is working. However, there is definitely an issue with CB. I notice you're using an older version of CB about 1.5 years old, I think), and it may be worth looking into upgrading that. I don't know if that will fix it though.
Some settings I tried to switch to fix the automatic activation (I undid these changes, but good to have note of what I tried):
* Removed the required field option from gender and school
* Turned off email confirmation (Joomla Configuration)
* Turned off Admin Approval Required (CB Configuration)
Again, sorry for the delay. I'll be focused more on this now that I've gotten in and seen the issue, and 3.1.2 is out, which fixes all known bugs for JFBConnect and frees us up a little more for these types of debug efforts.
Thanks!