Hi wal,
when creating a new encrypted folder, BoxCryptor (and also the portable version) creates a configuration file (.encfs6.xml) in the root of the encrypted folder where all encryption information is stored. Example:
New encrypted folder: D:\Documents\Encrypted
BoxCryptor creates the file D:\Documents\Encrypted\.encfs6.xml
It seems, BoxCryptor does not have write access to the encrypted folder.
--Robert