The category cache is (and always has been) off.
I'm sure there's nothing specific in the code that would duplicate the display of a category. I'm more sure that there's a database consistency problem, considering that only 7 of my users albums showed up before I ran a scan. I've had sporadic problems with albums appearing and disappearing over the years with Photopost and database scans seemed to have fixed that.
As for what I should have done, I did the best with what I could based on the available documentation, of which there is none. "Go search the forums" is fine and dandy, but isn't going to get you a canonical step-by-step approach to how to do things. I'm not digging at you as I know you have your hands full with coding, but in my very humble opinion you folks ought to go rework your documentation - especially when lots of folks are in the process of switching from vB
Right now I'm kind of stuck with a half-working gallery. I can restore from a backup, but to be honest I've restored and tried reintegrating a number of times, each time resulting in a different set of problems. Right now I'm trying to push people over to Flickr because I just want to be out of the gallery hosting business, but I can't pull the plug on the gallery quite yet.
So, what do you suggest I do to fix the situation?