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For anyone having issues with choices being reported incorrectly in Book Three: We've now found the reason for this bug, and we're pleased to say that it was not as all-encompassing as it first seemed to be! 
For further information, please see this post.
Thank you for all your help and patience. And for all the savegames that were sent to us in order to help us identify this bug. We're really grateful!
(Locking this thread to make sure we gather all replies in one thread. Please reply to this issue in the previously linked topic/post.)
