@Mouth I didn't read your post clearly enough
this isn't really what I was pointing out.
The issue is that when you make a usergroup joinable, then you go into any user's detail screen in the ACP, you will see the normal list of User Groups, and then you have a second set of User Groups that are joinable - the latter is simply a "mirror" or a subset of the normally configured usergroups. The problem is that let's say you have everyone in the Registered group as primary like you should and then you have a secondary user group called "blah" and you have 10000 users, 1000 of which are in "blah" as secondary (including yourself). Now you make that group joinable. Now go to one of those user screens, you will see that "blah" is checked, as it should be, but under the joinable groups it is not checked. Now go to your profile Join User Groups screen and you will see that even though you actually are in that user group, it still shows shows you the option to join it. So you have the appearance of not being in the group even though you are.
There is no database table that correlates the check box of the joinable user group. It is some random phantom check box setting and I can't figure out for the life of me how to take everyone who is in this above situation (they are part of the secondary group but not part of the joinable group) and fix that.