I think we can safely conclude that I have roughly the same problems as you do, on and off. Cloned FMs, banners disappearing, corrupted save games (I always keep mulptiple files, so that's never an issue for me), etc. Other people seem to have few or none of these problems.
I suggest we keep on reporting about these issues, it can only shed more light on what's actually happening. I've been thinking FD might be a potential troublemaker, but I'd find that very strange. Or perhaps, the move_character command, which might cause troubles with EB's differing naming schemes etc.
That was just brainstorming, BTW.
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