Still having a bad time. I installed CS6 3 times and always got the same problems above. Never got as far as opening InDesign CS6 at all. However, someone pointed me at Adobe's CS Cleaner Tool, so I cleaned out CS6 and, after a couple of weeks, tried to install again. It seemed to go well but when I tried to install plugins (Teacup's barcode and patterns for CS6, MultiFind/Exchange script etc.), Adobe Extension Manager came up and listed a slew of idcs6 extensions that 'failed to instal'. It'd be so helpful if it said why. Well, I tried again and it was ok.
Now I've just tried to amend a book originally set up in CS5.5. It opened the book ok, I ticked the Auto Document Conversion, amended one or two typos, added a page to one of the chapters: the book renumbered the following pages and crashed. Tried again. Crashed. Went back, got the book out of Time Machine, amended in CS5.5: good as gold.
So — should I only start new books in CS6? What about all the templates? Can I copy all the Para/Character Styles over if I open an empty/new document in CS6? Does CS6 not like CS5.5 documents?
At my wits' end at usual. But thanks for trying to help above.