Everything you place into an encrypted folder via the Boxcryptor drive is automatically also encrypted. If you create anything within an encrypted folder outside of the Boxcryptor (e.g. directly in Dropbox) it cannot be encrypted by Boxcryptor.
PS: Another reason could be a problem during synchronization. Encrypted folders contain a specific FolderKey.bch file with encrypted related information. If your cloud provider - for some reason - does not correctly sync such a file, the corresponding parent folder is not marked as encrypted anymore - any existing file stays encrypted but newly created files would not be encrypted anymore automatically (when the parent is not marked as encrypted).