I have had similar problems off and on...what I do to prevent them now is make a complete backup of the program directory. If the silly thing crops up, I just replace the current directory with the backup (I don't replace the save directory so I can maintain my map markers and macros). Simple fix for an annoying problem but I have no idea what goes wrong with the installation in the first place.
Edit
Just reread your post Sunflare and realized you had basically done this already.
Edit
Just reread your post Sunflare and realized you had basically done this already.
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Eldest, Order of the White Lotus