Ok, I've checked that in my library, in the file metadata.db, there are the conversion settings of each book.
I think I've solved the problem replacing with the Calibre folder configuration from a fresh installation the folder configuration after migration. This to avoid to have to manually re-import all my books after a fresh installation.
I'll check better if this really worked.
By the way, in what file are the settings stored? In special way, the setting about page size in conversion? There are may files in that folder.
Thanks for your support, btw.