I 'fixed' it by changing the names of the duplicate projects to BU(number). This obviously shouldn't happen. An easy way to filter it is that the ProjRef is NULL on the original project and the ID of that project on the backups. So there's the answer to the todo in the log files. Hope this helps!
Also, if you're going to dive in the save feature anyway to fix this, I'd really like a timer on screen to tell me when autosaves are coming. That way I don't find myself being interrupted in my work/train of thought every time that pops up while i'm working on something.