Hello,
I'm sorry for the confusion, but this is "just" a user interface glitch in Windows Explorer which sometimes occurs and which you can safely ignore.
Boxcryptor always detects if it should encrypt a file by the status of the parent directory. If the parent directory is encrypted, the file will be encrypted - if the parent directory is _not_ encrypted, the file will _not_ be encrypted (respectively a Boxcryptor window will pop up if you want to encrypt the file or not).
Best regards,
Robert