Just because your SkyDrive folder is available in the Boxcryptor Drive does not mean that it is encrypted. The Boxcryptor Drive shows all files - plaintext and encrypted ones. Encrypted files or folders are marked with a green font.
You can right-click any file or folder in your SkyDrive folder in the Boxcryptor Drive and choose "Boxcryptor -> Encrypt" to encrypt it. Only files you store in an encrypted folder are automatically encrypted.
Please see our "How it works" screencast for more information: