Double-clicking on a book usually opens that book on-disk -- it doesn't save it. Are you sure you actually used the save-to-disk menu?
It really is as simple as using the Save-to-disk menu icon, choosing a directory, and watching the progress bar as calibre saves a copy of all selected books. I haven't heard of anyone else failing to do so, so I am assuming user error.
But by all means, if you are convinced it is upgrading calibre that caused the problem, feel free to downgrade calibre -- all previous versions are available
HERE.