It sounds like you have been writing/copying files to the BoxCryptor.bc _folder_
in your local Box folder, instead of writing/copying files to your BoxCryptor-_drive_
In that case, you are storing normal, unencrypted files via the "normal" file-write or
-copy methods in the BoxCryptor.bc folder, but go around BoxCryptor.
By writing/copying to the BoxCryptor _drive_ (as defined when specifying the BoxCryptor.bc
folder location in BoxCryptor), you "pipe" your files through BoxCryptor for encryption.
Conversely, when reading from your BoxCryptor _drive_ you "pipe" the files through
BoxCryptor for decryption.